[galaxy-user] Chip-SEq S.cerevisiae IOn-Torrent
Hi everybody. I´m trying to analyze Chip-SEq Data from Ion-Torrent using Peak Calling/MACS. I have some questions: · How do I establish the Tag size? The median of size reads in my data are 156pb, the max 306? · Bandwidht: is the sonication size? Thanks in advance Regards ☺If you have used the Services of the Genomics Unit of Cabimer, we would be grateful if you would give us a mention in future publications Mónica Pérez Alegre, PhD Genomics Unit CABIMER-CSIC Edif. CABIMER - Avda. Américo Vespucio s/n Parque Científico y Tecnológico Cartuja 93 41092 Seville-SPAIN Tlf: +34 954 467 828 Fax: +34 954 461 664 www.cabimer.eshttp://www.cabimer.es/ http://www.cabimer.es/web/es/unidades-apoyo/genomica ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] ChIP-Seq Normalization to total number of reads
Hi Catheryn, for ChIP-seq analysis, normalisation and BAM file correlation we use deeptTools. Here you can read more about it: https://github.com/fidelram/deepTools And here is the toolshed repository: http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools Cheers, Bjoern Dear Galaxy, I am trying to analyze my ChIP-Seq data from Illumina using Galaxy. I have 2 datasets that I want to compare after normalizing each of them to their respective inputs, and these 2 datasets have very different number of reads to start with, is there a way to first normalize each dataset to total number of reads in Galaxy? Thanks. Your help is very much appreciated. Catheryn ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] ChIP-Seq Normalization to total number of reads
Dear Galaxy, I am trying to analyze my ChIP-Seq data from Illumina using Galaxy. I have 2 datasets that I want to compare after normalizing each of them to their respective inputs, and these 2 datasets have very different number of reads to start with, is there a way to first normalize each dataset to total number of reads in Galaxy? Thanks. Your help is very much appreciated. Catheryn ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] ChIP-seq data analysis question
Hello, My name is Christopher Terranova and am a M.S student at the University of Buffalo SUNY.I have been attempting to analyze my MACS data using Galaxy, already have my custom peaks on the UCSC Genome browser and have some specific questions. I am attempting to show how my peaks (and peak center coordinates) relate to gene units(+/-TSS and Genic) and intergenic regions specifically. I have been attempting to do this two different ways and am not sure if I am doing this correctly. Below I will list the steps I have been using with particular questions highlighted near my problem. I would also like to apologize for this extended e-mail, however, I have only been working with Galaxy for approx a month and attempting to figure all the manipulations is kind of difficult. If some can answer my questions I would greatly appreciate it!!! These questions relate specifically to promoters- 1.Retrieving TSS coordinates 1.Go to the UCSC genome browser, click Tables in the top of the page, and select mouse mm9 as the organism 2.select RefSeq genes in tracks, BED as the output format and check Send output to galaxy 3.click Get output then Send output to galaxy, and you are redirected to your Galaxy account, which contains an additional dataset 4.use the galaxy Filter tool (left column) to select all + strand genes 5.use the Cut tool (left column) to extract columns 1,2,2,4,5,6 (**is the c2 column repeated twice??**) in order to build a BED file containing the TSS for all + strand genes 6.do the same for the genes on the - strand Computing peak center coordinates 1.In Galaxy, select the tool Compute expression on every row in the left column (Text manipulation section) 2.as an expression, select c2+(c3-c2+1)/2, round result YES 3.select the dataset containing the peaks for one of the TFs (HNF4a or CBPA), and click execute; this creates a new dataset with an additional column containing the coordinate of the peak center. 4.now select the tool Cut, and extract the columns c1,c6,c6,c4,c5(**is the c6 column repeated twice??**) to create a new BED file containing the peak center 5.edit the metadata of this new dataset (clicking on the small pencil icon), and change the format to BED Computing distance to closest TSS 1.select the tool Fetch closest non-overlapping feature, select the new dataset containing the peak center coordinates, and the dataset containing the mouse TSS. A new dataset is created containing for each peak, the closest TSS 2.compute the distance from the peak center to the closest TSS using the Compute expression on every row tool(**what expression should I use to do this**) 3.plot the distribution using the Histogram of a numeric column tool. Secondary way: I understand this is not identifying the peak center closest to the TSS or a particular strand, however, still have a couple questions? Now we have a data set corresponding to all human RefSeqs (34,765) and we want to convert this set into one corresponding to human promoter regions. First, we will make sure our data set just contains the start and end coordinates of the genes. Select the Text Manipulation tool and then Cut colums from a table. Set cut columns to c1,c2,c3,c4,c6 (**Is this the right c1... conformation??**). Make sure our previously downloaded RefSeq tdat set is selected and click on Execute. When this is finished, click on the pencil icon to assign names to the columns. Set name to RefSeqs, click save and change the data type to interval and click save. Now click the pencil icon again to define the columns. Set the start column to 2 and the end column to 3, the strand column to 5 and the Name/Identifier column to 4 and click on save. Now, go to the Operate on Genomic Intervals section of the Tools menu and select Get flanks to get the flanking regions for the RefSeq data set we just created. Make sure our RefSeq data set is selected and we want to get the upstream flanking regions for this data set. Set the length of the flanking region to 1000 to get the coordinates for 1kb upstream. Later on we could use different intervals. Click on Execute. When this has finished, go to Operate on Genomic Intervals again and select Join. Now set First query to Get flanks.. and Second query to the peaks file of the MACS output and then click on Execute. We now end up with 710 regions where our ChIP-Seq peaks overlap with our 1kb upstream region (promoter region). Lastly, while not discussed here, what exactly does the offset command do when getting flanks? Thank you very much and again, I apologize for the extensive questions! Sincerely, Christopher Terranova ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy
Re: [galaxy-user] Chip-seq exercise
Hi Dan - I agree this tutorial is very helpful. In running through this exercise recently, however, I noticed a few very small things that could help improve this already excellent tutorial for new users: 1) you may want to explicitly tell people to create an account first if they haven't so they can do the workflow parts without having to create and account in midstream. 2) change reads have been reduced to those mapping to chr9 to reads have been reduced to those mapping to chr19 -- fix typo 3) change Click the 'import this dataset' button above to add this dataset to Click the green circle with a + to the right of 'import this dataset' button above to add this dataset -- make the location of the import button more explicit 4) change to your analysis history to being the analysis to to your analysis history to begin the analysis -- fix typo 5) change You will need to change the reference genome build you are mapping against to mm9 to You will need to change the reference genome build you are mapping against to Mouse (Mus musculus): mm9 Full -- make instructions about which version of mm9 to use more explicit 6) change Select your previous CTCF dataset for ChIP-seq tag file to Set your tag size to the same value as before and select your previous CTCF dataset -- add reminder to set tag size again Best regards, Casey On 22 Mar 2012, at 13:38, Daniel Blankenberg wrote: Hi Josh, Thank you for reporting this issue, it has been resolved. Please let us know if you encounter additional problems in the future. Thanks for using Galaxy, Dan On Mar 21, 2012, at 8:18 PM, Joshua Udall wrote: Does anyone know what happened to the chip-seq exercise by James? It was part of a collection here: http://main.g2.bx.psu.edu/u/james/p/exercises and it was linked here: http://main.g2.bx.psu.edu/u/james/p/exercise-chip-seq But is it 'Not Found'. It was a very useful exercise. Will it be back soon? Josh ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Chip-seq data
Giuseppe, Your ChipSeq data is already in fastq format. It appears to have Illunima quality scores, so you'll need to use the NGS:QC and manipulation FASTQ Groomer tool, using 'Illumina 1.3+' as input and 'Sanger' quality format as output. As to using MACS, I've never used it before but you should be able to get your answers by reading the manual at: http://liulab.dfci.harvard.edu/MACS/README.html Hope this helps, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 29/11/2011 15:16, Giuseppe Petrosino petros...@ceinge.unina.it wrote: Hi,I have illumina ChipSeq data in txt format with this structure: @HWI-EAS225:8:1:1:58#0/1 NAGAGTGCCCGGGTTCAGTTCTCAGCACCCATGTGG +HWI-EAS225:8:1:1:58#0/1 DMSSUSSTTTUTSRQRTTTSSSUS @HWI-EAS225:8:1:1:1803#0/1 NCCATGGGAAGAGCTGGGCAGGCGGGCCGAGCGAAG +HWI-EAS225:8:1:1:1803#0/1 DLSTTSKOUTRRTTSSSSRPNNTOJOTSSRTB @HWI-EAS225:8:1:1:1547#0/1 NAGGGGTGGGACTGGCACTTGCCTCTACCAGC +HWI-EAS225:8:1:1:1547#0/1 DLVVVTPTUVVWVVUVVUWVVVWWWVVV Can I convert into Fastq format?If so, how can I? Furthermore, after using Map with Bowtie for Illumina, how can I use MACS (Model-based Analysis of ChIP-Seq) if I have two files for IP samples and two files for Control samples? Thank you so much. Giuseppe ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Chip-seq data
Hi, I have illumina ChipSeq data in txt format with this structure: @HWI-EAS225:8:1:1:58#0/1 NAGAGTGCCCGGGTTCAGTTCTCAGCACCCATGTGG +HWI-EAS225:8:1:1:58#0/1 DMSSUSSTTTUTSRQRTTTSSSUS @HWI-EAS225:8:1:1:1803#0/1 NCCATGGGAAGAGCTGGGCAGGCGGGCCGAGCGAAG +HWI-EAS225:8:1:1:1803#0/1 DLSTTSKOUTRRTTSSSSRPNNTOJOTSSRTB @HWI-EAS225:8:1:1:1547#0/1 NAGGGGTGGGACTGGCACTTGCCTCTACCAGC +HWI-EAS225:8:1:1:1547#0/1 DLVVVTPTUVVWVVUVVUWVVVWWWVVV Can I convert into Fastq format?If so, how can I? Furthermore, after using Map with Bowtie for Illumina, how can I use MACS (Model-based Analysis of ChIP-Seq) if I have two files for IP samples and two files for Control samples? Thank you so much. Giuseppe ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] ChIP seq on BED file
Jen, I ran the flow as you suggested, but got following error message, Do You hav eany suggestion? I added 0 and flips the columns: Here is the few lines of input file: chr1 12137 12336 61R33AAXX100706:1:79:7707:9270 0 - chr1 31542 31741 61R33AAXX100706:1:37:11341:10600 1 - chr1 39921 40120 61R33AAXX100706:1:2:16103:17629 2 - chr1 93213 93412 61R33AAXX100706:1:113:14396:2056 3 - chr1 109395 109594 61R33AAXX100706:1:13:8451:9619 4 - chr1 146854 147053 61R33AAXX100706:1:53:15558:13513 5 -Te error message is as followINFO @ Fri, 30 Sep 2011 17:59:54: # ARGUMENTS LIST: # name = macs_output # format = BED # ChIP-seq file = /data/CistromeAP/galaxy_database/files/000/198/dataset_198187.dat # control file = None # effective genome size = 2.79e+09 # band width = 300 # model fold = 10,30 # pvalue cutoff = 1.00e-05 # Small dataset will be scaled towards larger dataset. # Range for calculating regional lambda is: 1 bps INFO @ Fri, 30 Sep 2011 17:59:54: #1 read tag files... INFO @ Fri, 30 Sep 2011 17:59:54: #1 read treatment tags... INFO @ Fri, 30 Sep 2011 18:00:02: 100 INFO @ Fri, 30 Sep 2011 18:00:11: 200 INFO @ Fri, 30 Sep 2011 18:00:21: 300 INFO @ Fri, 30 Sep 2011 18:00:30: 400 INFO @ Fri, 30 Sep 2011 18:00:39: 500 Traceback (most recent call last): File /usr/local/bin/macs14, line 358, in module main() File /usr/local/bin/macs14, line 60, in main (treat, control) = load_tag_files_options (options) File /usr/local/bin/macs14, line 330, in load_tag_files_options treat = tp.build_fwtrack() File /usr/lib/python2.6/dist-packages/MACS14/IO/Parser.py, line 150, in build_fwtrack (chromosome,fpos,strand) = self.__fw_parse_line(thisline) File /usr/lib/python2.6/dist-packages/MACS14/IO/Parser.py, line 187, in __fw_parse_line raise StrandFormatError(thisline,thisfields[5]) MACS14.IO.Parser.StrandFormatError: 'Strand information can not be recognized in this line: chr2\t121859840\t121860039\t61R33AAX\t.\t5837743,5837743' Thanks Vasu --- On Fri, 9/30/11, Jennifer Jackson j...@bx.psu.edu wrote: From: Jennifer Jackson j...@bx.psu.edu Subject: Re: [galaxy-user] BED to BAM conversion in Galaxy To: shamsher jagat kanwar...@gmail.com Cc: galaxy-u...@bx.psu.edu Date: Friday, September 30, 2011, 9:08 AM Hello, The format of the BED file may be a problem. To be in BED format, an additional field is required for the score attribute. This would be column 5, moving the strand out to column 6. To do this: 1 - use Text Manipulation-Add column with the value 0 note: 0 often is used to represent a NULL or undefined score value in BED files. This field cannot be left as whitespace (two tabs), a placeholder value must be present. 2 - then use Text Manipulation-Cut and cut out the columns in the proper BED file order, in this case c1,c2,c3,c4,c6,c5, to swap the last two 3 - change datatype to BED using the pencil icon/Edit attributes form In Galaxy, many of the tools in NGS: Peak Calling will work with ChIP-seq data in BED format. Having a control would be helpful, but is not required by all tools. Good luck with your project, Jen Galaxy team On 9/29/11 9:31 PM, shamsher jagat wrote: Thanks Jen, My problem is I have ChIP-seq data where I have one Bed file with coordinates- chr172402772422661PDWAAXX100706:4:19:6952:18071- Then there is wig file.? Is it possible that thsi data can be analyzed in Galaxy/ Cistrome. I tried to use Cistrome which gav eme error message. Thanks On Wed, Sep 28, 2011 at 3:46 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hello, It is possible to go from SAM/BAM to BED, but not the reverse. SAM/BAM files contain the actual sequence data associated with the original aligned read. BED files only have the reference genome location of the alignment (no read sequence). It is possible to extract genomic sequence based on BED coordinates, but the resulting sequence would not necessarily be the same sequence as in the original aligned read (any variation would be lost). BED is very similar to Interval format, so Interval tools also work with BED format. A BED file is basically a 3-12 column, tab delimited file, so tools that work with Tabular data are also appropriate for BED file. Note that you may need to change the datatype to be interval or tab for certain tools to recognize a BED file as an input. Hopefully this helps, Jen Galaxy team On 9/22/11 2:55 PM, shamsher jagat wrote: Is it possible to use some tool in Galaxy to convert BED file to Bam/ sam file. In other word do we have Bed tools or other option in Galaxy Thanks _ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server
[galaxy-user] ChIP seq on BED file
Hello Vasu, The score value should be 0 for each row. When adding the new column, set Iterate?: to the default no. It also looks like there may be some inconsistencies in the original file. Are you certain it is 5 columns (exactly) for every row? Including the error row reported? Some detective work to get the file in the right format is probably necessary. Tabs are good to check. Change the filetype to tabular, run the file through the Convert delimiters to TAB tool using Convert all: whitespace, next run Condense consecutive characters to cleanup any trailing tabs, then change the filetype back to BED and assign the score column on the Edit Attributes form (pencil icon). Hopefully this helps, Jen Galaxy team On 9/30/11 3:13 PM, vasu punj wrote: Jen, I ran the flow as you suggested, but got following error message, Do You hav eany suggestion? I added 0 and flips the columns: Here is the few lines of input file: chr112137 12336 61R33AAXX100706:1:79:7707:9270 0 - chr131542 31741 61R33AAXX100706:1:37:11341:106001 - chr139921 40120 61R33AAXX100706:1:2:16103:17629 2 - chr193213 93412 61R33AAXX100706:1:113:14396:20563 - chr1109395 109594 61R33AAXX100706:1:13:8451:9619 4 - chr1146854 147053 61R33AAXX100706:1:53:15558:135135 - Te error message is as follow INFO @ Fri, 30 Sep 2011 17:59:54: # ARGUMENTS LIST: # name = macs_output # format = BED # ChIP-seq file = /data/CistromeAP/galaxy_database/files/000/198/dataset_198187.dat # control file = None # effective genome size = 2.79e+09 # band width = 300 # model fold = 10,30 # pvalue cutoff = 1.00e-05 # Small dataset will be scaled towards larger dataset. # Range for calculating regional lambda is: 1 bps INFO @ Fri, 30 Sep 2011 17:59:54: #1 read tag files... INFO @ Fri, 30 Sep 2011 17:59:54: #1 read treatment tags... INFO @ Fri, 30 Sep 2011 18:00:02: 100 INFO @ Fri, 30 Sep 2011 18:00:11: 200 INFO @ Fri, 30 Sep 2011 18:00:21: 300 INFO @ Fri, 30 Sep 2011 18:00:30: 400 INFO @ Fri, 30 Sep 2011 18:00:39: 500 Traceback (most recent call last): File /usr/local/bin/macs14, line 358, inmodule main() File /usr/local/bin/macs14, line 60, in main (treat, control) = load_tag_files_options (options) File /usr/local/bin/macs14, line 330, in load_tag_files_options treat = tp.build_fwtrack() File /usr/lib/python2.6/dist-packages/MACS14/IO/Parser.py, line 150, in build_fwtrack (chromosome,fpos,strand) = self.__fw_parse_line(thisline) File /usr/lib/python2.6/dist-packages/MACS14/IO/Parser.py, line 187, in __fw_parse_line raise StrandFormatError(thisline,thisfields[5]) MACS14.IO.Parser.StrandFormatError: 'Strand information can not be recognized in this line: chr2\t121859840\t121860039\t61R33AAX\t.\t5837743,5837743' Thanks Vasu --- On *Fri, 9/30/11, Jennifer Jackson /j...@bx.psu.edu/* wrote: From: Jennifer Jackson j...@bx.psu.edu Subject: Re: [galaxy-user] BED to BAM conversion in Galaxy To: shamsher jagat kanwar...@gmail.com Cc: galaxy-u...@bx.psu.edu Date: Friday, September 30, 2011, 9:08 AM Hello, The format of the BED file may be a problem. To be in BED format, an additional field is required for the score attribute. This would be column 5, moving the strand out to column 6. To do this: 1 - use Text Manipulation-Add column with the value 0 note: 0 often is used to represent a NULL or undefined score value in BED files. This field cannot be left as whitespace (two tabs), a placeholder value must be present. 2 - then use Text Manipulation-Cut and cut out the columns in the proper BED file order, in this case c1,c2,c3,c4,c6,c5, to swap the last two 3 - change datatype to BED using the pencil icon/Edit attributes form In Galaxy, many of the tools in NGS: Peak Calling will work with ChIP-seq data in BED format. Having a control would be helpful, but is not required by all tools. Good luck with your project, Jen Galaxy team On 9/29/11 9:31 PM, shamsher jagat wrote: Thanks Jen, My problem is I have ChIP-seq data where I have one Bed file with coordinates- chr172402772422661PDWAAXX100706:4:19:6952:18071- Then there is wig file.? Is it possible that thsi data can be analyzed in Galaxy/ Cistrome. I tried to use Cistrome which gav eme error message. Thanks On Wed, Sep 28, 2011 at 3:46 PM, Jennifer Jackson j...@bx.psu.edu http://us.mc1147.mail.yahoo.com/mc/compose?to=j...@bx.psu.edu mailto:j...@bx.psu.edu http://us.mc1147.mail.yahoo.com/mc/compose?to=j...@bx.psu.edu wrote: Hello, It is possible to go from SAM/BAM to BED, but not the reverse. SAM/BAM files contain the actual sequence data associated with the original aligned read.
[galaxy-user] Chip-seq
Can I analyze two bed files from Chip seq experiemnt in Galaxy? I have one file of input and other of sample. Both these files have peak locations. Any suggestion of a work flow in Galaxy? ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Chip-Seq, Encode Peaks and Galaxy
Hi Rad, Jorge, Sorry for the delay in reply. We have not yet released a pre-canned workflow to do this. However, if you are looking to associate one set of Genomic interval/region data with another set, Galaxy's interval operation tools are a good place to begin. There are good examples of using these tools available through screencasts (http://galaxycast.org), Galaxy 101 (http://usegalaxy.org/galaxy101), as well as the wiki (http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations). Please let us know if we can provide additional information. Thanks for using Galaxy, Dan On Jun 23, 2011, at 9:41 AM, Radhouane Aniba wrote: Thanks Jennifer Rad 2011/6/23 Jorge Andrade andrade.jo...@gmail.com Please keep me on the loop as I am also interested in similar workflow. Many thanks and best regards, Jorge On Thu, Jun 23, 2011 at 3:21 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Rad, Dan will be able to help you get started and build up a workflow for your analysis. He is currently on vacation, but will be returning soon and will contact you directly when he returns. We are very sorry about the delayed reply. Please know that we definitely want to help you to use Galaxy for your project, We will be in touch, Best, Jen Galaxy team On 6/17/11 10:55 AM, Radhouane Aniba wrote: Hi everyone, I have a list of genomic regions with some variants and would like to study the correlation between theses variants and epigenomics marks such as histone modifications. From Encode download page, i got some files corresponding to peaks of these hsitone modifications and would like to know if there is a way to create a pipeline using galaxy to map my variants, depending on genomic regions to the information I have from the histone modification peaks. Is there someone who can point me to a step by step to do things to start using Galaxy ? Thank you Rad ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Radhouane Aniba Bioinformatics Postdoctoral Research Scientist Institute for Advanced Computer Studies Center for Bioinformatics and Computational Biology (CBCB) University of Maryland, College Park MD 20742 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Chip-Seq, Encode Peaks and Galaxy
Please keep me on the loop as I am also interested in similar workflow. Many thanks and best regards, Jorge On Thu, Jun 23, 2011 at 3:21 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Rad, Dan will be able to help you get started and build up a workflow for your analysis. He is currently on vacation, but will be returning soon and will contact you directly when he returns. We are very sorry about the delayed reply. Please know that we definitely want to help you to use Galaxy for your project, We will be in touch, Best, Jen Galaxy team On 6/17/11 10:55 AM, Radhouane Aniba wrote: Hi everyone, I have a list of genomic regions with some variants and would like to study the correlation between theses variants and epigenomics marks such as histone modifications. From Encode download page, i got some files corresponding to peaks of these hsitone modifications and would like to know if there is a way to create a pipeline using galaxy to map my variants, depending on genomic regions to the information I have from the histone modification peaks. Is there someone who can point me to a step by step to do things to start using Galaxy ? Thank you Rad __**_ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/**listinfo/galaxy-devhttp://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ __**_ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/**listinfo/galaxy-devhttp://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Chip-Seq, Encode Peaks and Galaxy
Thanks Jennifer Rad 2011/6/23 Jorge Andrade andrade.jo...@gmail.com Please keep me on the loop as I am also interested in similar workflow. Many thanks and best regards, Jorge On Thu, Jun 23, 2011 at 3:21 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Rad, Dan will be able to help you get started and build up a workflow for your analysis. He is currently on vacation, but will be returning soon and will contact you directly when he returns. We are very sorry about the delayed reply. Please know that we definitely want to help you to use Galaxy for your project, We will be in touch, Best, Jen Galaxy team On 6/17/11 10:55 AM, Radhouane Aniba wrote: Hi everyone, I have a list of genomic regions with some variants and would like to study the correlation between theses variants and epigenomics marks such as histone modifications. From Encode download page, i got some files corresponding to peaks of these hsitone modifications and would like to know if there is a way to create a pipeline using galaxy to map my variants, depending on genomic regions to the information I have from the histone modification peaks. Is there someone who can point me to a step by step to do things to start using Galaxy ? Thank you Rad __**_ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/**listinfo/galaxy-devhttp://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ __**_ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/**listinfo/galaxy-devhttp://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- *Radhouane Aniba* *Bioinformatics Postdoctoral Research Scientist* *Institute for Advanced Computer Studies Center for Bioinformatics and Computational Biology* *(CBCB)* *University of Maryland, College Park MD 20742* ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Chip-Seq, Encode Peaks and Galaxy
Hello Rad, Dan will be able to help you get started and build up a workflow for your analysis. He is currently on vacation, but will be returning soon and will contact you directly when he returns. We are very sorry about the delayed reply. Please know that we definitely want to help you to use Galaxy for your project, We will be in touch, Best, Jen Galaxy team On 6/17/11 10:55 AM, Radhouane Aniba wrote: Hi everyone, I have a list of genomic regions with some variants and would like to study the correlation between theses variants and epigenomics marks such as histone modifications. From Encode download page, i got some files corresponding to peaks of these hsitone modifications and would like to know if there is a way to create a pipeline using galaxy to map my variants, depending on genomic regions to the information I have from the histone modification peaks. Is there someone who can point me to a step by step to do things to start using Galaxy ? Thank you Rad ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Chip-Seq, Encode Peaks and Galaxy
Hi everyone, I have a list of genomic regions with some variants and would like to study the correlation between theses variants and epigenomics marks such as histone modifications. From Encode download page, i got some files corresponding to peaks of these hsitone modifications and would like to know if there is a way to create a pipeline using galaxy to map my variants, depending on genomic regions to the information I have from the histone modification peaks. Is there someone who can point me to a step by step to do things to start using Galaxy ? Thank you Rad ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
