Re: [galaxy-user] question history

2014-04-01 Thread Jennifer Jackson
Hello Liesbeth, Hopefully you are no longer having this problem, but we wanted to follow-up. From our view of your account, all histories are accessible on the Main public Galaxy server at http://usegalaxy.org. Our sincere apologies for transient usage issues that occurred around the time

[galaxy-user] question history

2014-03-31 Thread Liesbeth Van Rompay
Hi, Although I am occupying 91% of my space on the Galaxy platform, since Galaxy was out, I cannot access my history anymore. No error message appears. What can I do? Best regards, Liesbeth ___ The Galaxy User list should be used for the

[galaxy-user] Question regarding storage space

2014-03-27 Thread Alexandre Maia
I am using Deeptools at the main public server and was adding some files initially to test. Now I have removed all my files (hidden and unhidden) and history, but my usage is still at 38%. How can I remove all the files to have a 0%? My user name is alexandre.gaspar.m...@gmail.com Thanks. A

Re: [galaxy-user] Question regarding storage space

2014-03-27 Thread Jennifer Jackson
Hello, Please check all histories and shared histories. All data must be permanently deleted, and no histories shared with you, to reach 0% usage. Find all in the in the history menu under: * Saved histories - Advanced search - status = all or deleted' * Histories shared with me Help is

Re: [galaxy-user] Question in converting gtf file for p_id

2014-01-21 Thread Jennifer Jackson
Hello Nancy, The attribute sounds as if it is the correct place in the reference annotation file (the 9th field), but perhaps there are other format/content problems with the file. Do you have a tss_id? Do you have exons labeled? This is the area of the manual that covers the formatting and

Re: [galaxy-user] Question in converting gtf file for p_id

2014-01-21 Thread Yanxiang Shi
Hi Jennifer, I did see tss_id in my results and also exon labels. The tss_id was assigned during the calculation, having the numbers tss1, tss2, etc. By saying writing codes I mean such as in the link you sent to me, there is: *Note: *If an arbitrary GTF/GFF3 file is used as input (instead of

Re: [galaxy-user] Question in converting gtf file for p_id

2014-01-21 Thread Jennifer Jackson
Hi Nancy, It is not quite clear in which steps you used the reference annotation or how these attributes were lost exactly. Cuffcompare is a tool in Galaxy - but before we go any further I think that examining the history would be the speedest path to a solution. Would you share a history

[galaxy-user] Question in converting gtf file for p_id

2014-01-18 Thread Yanxiang Shi
Hi all, I've been trying to use the cufflinks-cuffmerge-cuffdiff flow to analyze my RNAseq data. However, cuffmerge lost my p_id. My p_id was originally from changing the protein_id to p_id by myself in the gtf file. The current p_id showed up in the same attributes column as gene_id in the gtf

[galaxy-user] Question on uploading and use .bam files

2013-12-04 Thread Lu, Yuan (MU-Student)
Dear Sir or Madam, Recently I was trying to use Galaxy for my data analysis but ran into problems. Condition: I used galaxy server at PSU. I tried load local .bam file directly to galaxy, I also tried FTP, but both ways resulted into the same outcome. The .bam files I was using are pure

Re: [galaxy-user] Question on uploading and use .bam files

2013-12-04 Thread Jennifer Jackson
Hello L.Y., I just tested .bam upload using FTP (with the client FileZilla) and all went fine. Just to confirm, you are using the public Main Galaxy server at http://usegalaxy.org? Many of our services were down for several hours yesterday for maintenance related reasons - if you upload

[galaxy-user] question about samtools in Galaxy

2013-10-02 Thread Robert Jackman
Hi, Can anyone tell me if the ability to randomly sample a sam or bam file (view -s) is available via Galaxy samtools? I can't find it but it might be an option that I am missing. sincerely, Robert Jackman rais...@gmail.com rjack...@bu.edu

Re: [galaxy-user] question about samtools in Galaxy

2013-10-02 Thread Jennifer Jackson
Hi Robert, This function is not wrapped into a tool yet by the dev team. I checked the Tool Shed as well and didn't see it there. But there is another option to get to the same result. The tool Text Manipulation - Select random lines from a file can be used with a SAM file. Don't not use

[galaxy-user] question

2013-09-25 Thread Bondici, Ibi
On the FastUnifrac webside available at the begining of the year I was able to obtain p-values having “unifrac_env.txt”file, GreenGene Core as the reference tree and “Automatically generate category mapping file” option was previously available. Can I have access to the previous

Re: [galaxy-user] question

2013-09-25 Thread Jennifer Jackson
Hello Vioricia, For this question, it would be best to contact the team that is hosting the public Galaxy site, as these are tools custom to their server. The contact information is on the bottom of the home page: http://unifrac.colorado.edu/ Best! Jen Galaxy team On 9/25/13 1:13 PM,

[galaxy-user] Question about expression in Galaxy tools

2013-08-29 Thread 师云
Hello everyone, I found regular expression could be available in the tool (filter and sort) -Filter. I wonder whether it could be the same in the tool (Text Manipulation) -Compute. I have checked that the fuction len(c4.split('_')) would return error. So, could anyone tell me if it was

Re: [galaxy-user] Question about expression in Galaxy tools

2013-08-29 Thread Jennifer Jackson
Hello, There are some tools in the group 'Text Manipulation' that do this sort of manipulation directly. Combined, many basic unix functions can be performed. Combine them to create custom tools using Workflows - even place them in your tool menu for seamless access. To move from file A to

[galaxy-user] Question about Extract intron sequences from [gtf file] + [genome FASTA file]

2013-08-20 Thread 师云
Dear Jen, I am not much of a Galaxy user yet. Some days ago I know something about Galaxy and found it a really wonderful tool. And I am confused by a simple question regarding how to extract intron sequences from [gtf file]; Here is a simple of a gtf file: 1 Cufflinks transcript322

Re: [galaxy-user] question

2013-08-05 Thread Jennifer Jackson
Hello Larry, The Manipulate Fastq tool only brings up the regular trimmer tools again once sequence and trim are selected, so this will not work. And a regular expression could be used as a filter, but that will not actually trim the data. If you choose to filter, this regular expression

[galaxy-user] question

2013-07-28 Thread Larry Simpson
Hi Is it possible to trim a variable number of a specific nucleotide from the 3' ends of fastq RNA reads? The Manipulate Fastq utility in Galaxy may have this ability but I do not know how to create a custom inquiry. Thanks in advance for any assistance. Larry

Re: [galaxy-user] question

2013-07-28 Thread Ido Tamir
You could use the adaptor clip with e.g. a custom poly-A 'adaptor' its in FASTX-Toolkit for FASTQ data best, ido On Jul 28, 2013, at 8:44 PM, Larry Simpson larrys3...@gmail.com wrote: Hi Is it possible to trim a variable number of a specific nucleotide from the 3' ends of fastq RNA

[galaxy-user] Question on megablast databases

2013-05-24 Thread Sun, Wenping [USA]
Dear galaxy members, I have a question on the databases used in megablast module from galaxy. There are four db options to blast against with - 1. htgs 28-Jan-2013 2. nt 28-Jan-2013 3. wgs 28-Jan-2013 4. phiX174 Is there any further information to guide which database

Re: [galaxy-user] Question on megablast databases

2013-05-24 Thread Jennifer Jackson
Hi Kathryn, These first three are three different types of sequence databases available from GenBank The last is a genome assembly for the phiX174 genome. Information about all can be found here: http://www.ncbi.nlm.nih.gov/genbank/ There are many uses, one example is covered in our

Re: [galaxy-user] Question on galaxy data visualization

2013-05-13 Thread Jennifer Jackson
Hello Kathryn, Trackster is the primary data visualization tool and can be accessed by clicking on the mini graph icon within a dataset: or by going to "Visualization" in the upper menu bar and starting a new track browser.

[galaxy-user] Question about scripting

2013-04-19 Thread leconte
hello, My subject is at the border between Galaxy and Condor I'found method to use Galaxy with condor cluster solution. In fact I have wrote a script when Galaxy call clustalw2 , it calls in fact a script called clustalw2. All run exactly as I want excepting ... but Galaxy get in error and

Re: [galaxy-user] Question about tool

2013-03-27 Thread Jennifer Jackson
Hi Sandra, Galaxy can certainly be used to correlate a set of unknown genomic coordinates with another annotated set of genomic corrdinates, such as those available from UCSC, Biomart, etc. The tool set to look at is Operate on genomic intervals and an example of how these tools are used,

[galaxy-user] Question about tool

2013-03-25 Thread Sandra Santos
Hi My name is Sandra and I'm a curator of a database of transcriptional relationships in yeast. We are doing our annual update, and in one paper I found a number of ChIP-seq results. Unfortunately, the authors only included in the supplemental information the genome coordinates, but no

[galaxy-user] question on galaxy reference genome window

2012-12-19 Thread Sun, Wenping [USA]
Dear Galaxy members, I am new to galaxy and just installed galaxy on aws cloud. I am testing how it works and have the following question below: 1. I tried to test bowtie2 with the dataset I uploaded, however, the window for reference genome is very narrow and nothing from pull-down

Re: [galaxy-user] Question about Unified genotyper

2012-08-07 Thread Carlos Borroto
Hi Mathew, Regarding 1 you might want to read this thread: http://user.list.galaxyproject.org/Problem-with-Depth-of-Coverage-on-BAM-files-GATK-tools-td4654147.html All tools from GATK are limited to hg_g1k_v37 as far as I know. Best, Carlos On Mon, Aug 6, 2012 at 10:30 AM, Mathew Bunj

Re: [galaxy-user] Question about Unified genotyper

2012-08-07 Thread Jennifer Jackson
Hello Mathew, Carlos is correct the the tools in the group NGS: GATK Tools (beta) will require that the data is mapped/associated with the reference genome hg_g1k_v37. Belinda has offered to help with the details that go beyond Galaxy and that is great - the GATK forum is definitely the best

Re: [galaxy-user] Question about SICER out put

2012-08-07 Thread Jennifer Jackson
Hi Kanwar, I found that you also posted this question and another like to the Google group for SICER on 7/10 and received some help there: http://groups.google.com/group/sicer-users Glad that you were able to get the questions resolved. For others reading this post or interested in SICER

[galaxy-user] Question about SICER out put

2012-07-10 Thread shamsher jagat
I used SICR to call peaks and have following out put files: 1. test.1removed bed 2. control1 removed .bed 3. test w 200 graph 4. test w200 normalized graph 5. test w200-G600 FDR.05 island.bed 6. test w200-G600 FDR .05 island filtered.bed 7. test w200-G600 FDR .05 island filtered normalized.wig

[galaxy-user] Question about Galaxy

2012-06-08 Thread Jennifer Jackson
Hi Qianli, It looks as if you are using the Extract DNA tool? GTF/GFF files have coordinates with a 1-based start position - and this was your input, but the output from this tool produces coordinates with a BED-style 0-based start position. The genome index files used by the tool are in

[galaxy-user] Question about fetching sequence from genome

2012-05-30 Thread Qianli Shen
Hi I want to fetch sequence from soybean genome, according to a gff file. My gff3 file and genome file are attached to the email, because it is not easy to recongnize the format if I paste it in the email. And it keeps reporting the error: An error occurred running this job: Traceback (most

[galaxy-user] Question about extracting information from CEAS run results

2012-05-18 Thread shamsher jagat
I have run a ChIPseq work flow in galaxy, At teh end I ran CEAS: Enrichment on chromosome and annotation (version 1.0.0) to annotate the peaks which gave me a pdf file shoiwng distribution of peaks across genome with pie chart as well as well as histogram. It shows that ~5% of my peaks in 5UTR

[galaxy-user] Question about megablast

2012-04-09 Thread shamsher jagat
I have a question about megablast, I want to megablast my seq: the databases mentioned include (against target databases): htgs27 nt27 wgs 09 phiX174 How can I find details about these databases and which one is human or mouse or may be best for my case. Thanks Vasu

Re: [galaxy-user] Question about megablast

2012-04-09 Thread Jennifer Jackson
Hello Vasu, These databases contain sequences from all species in the divisions. The number indicates the release version. The actual source is: ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/ A description of each division's contents can be found at: http://www.ncbi.nlm.nih.gov/genbank The

Re: [galaxy-user] Question about plotting circos plot

2012-03-14 Thread Jennifer Jackson
Hello Shamsher, Another user posted that they have started a Galaxy wrapper for the Circos tool itself, but I wanted to let you know about the tool EMBOSS - cirdna: Draws circular maps of DNA constructs. The link on the tool's form points to all of the EMBOSS tools, including this specific

Re: [galaxy-user] question from a new Galaxy user

2012-03-09 Thread Kevin L
If I may add, I believe galaxy will uncompress your files if zipped. Unzipping a 13 GB file, will take a while. Kev ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at

[galaxy-user] Question about aaChange tool.

2012-03-09 Thread Maha Al Kahtani
Hello, Recently i have used galaxy to find corresponding amino acids to a list of SNPs that i have. i used aaChange tool from the tool panel for this purpose. After obtaining the result i checked the correctness of this results by searching dbSNP for randomly chosen SNPs. however, some of those

Re: [galaxy-user] Question about aaChange tool.

2012-03-09 Thread Jennifer Jackson
Hello Maha, This does sound very strange. Would you please share a link to your history so that we can examine the data and determine where the problem originates? Please note which dataset contains this particular problem if there are several runs from this same tool. Use Options - Share

Re: [galaxy-user] Question about plotting circos plot

2012-03-07 Thread Björn Grüning
Hi Shamsher. We have a small initial wrapper for circos. Its not complete yet and we are not sure if its even possible to wrap such a complex tool in a good galaxy UI. But if you are interested i can share our code. Cheers, Bjoern I wonder if is it possible to visualize mutation data in

[galaxy-user] Question about plotting circos plot

2012-03-06 Thread shamsher jagat
I wonder if is it possible to visualize mutation data in circular plot termed as circos plot e.g @http://www.eurekalert.org/multimedia/pub/31019.php?from=181881 Any suggestion for an alternative tool will also be appreciated. Thanks Shamsher

[galaxy-user] Question about uploading custom index for bowtie

2012-02-06 Thread William Light
I recently tried to upload a custom made index for bowtie using Filezilla as my FTP source, but I got an error message, I think due to the autodetect for file type not recognizing this file type. Is there something special that I should do to upload my six .ebwt files for my reference?

Re: [galaxy-user] Question about uploading custom index for bowtie

2012-02-06 Thread Jennifer Jackson
Hello William, To use a custom reference genome, all you need to upload is the single fasta file for the genome. Galaxy will do the rest and create indexes as appropriate. Hopefully this helps! Thanks, Jen Galaxy team On 2/6/12 11:51 AM, William Light wrote: I recently tried to upload a

[galaxy-user] Question re: Quota not re-setting after data deletion

2011-12-07 Thread Mcgowen, Michael
Hello, I'm using the Galaxy Main --I was trying to groom data that I had uploaded at about 11 AM EST and Galaxy informed me that I had met my quota. Indeed it said that my quota was 98% full, but my history (my only one) said that I had about 13 Gb-- I deleted everything in my history in

Re: [galaxy-user] Question re: Quota not re-setting after data deletion

2011-12-07 Thread Jennifer Jackson
Hello Michael, Data will count towards the disk quota when not permanently deleted. Also, once permanently deleted, it will take a bit of time (less than an hour to several hours) for the disk counts in the UI to update. Perhaps this has already been resolved, but if not, hopefully the rest

Re: [galaxy-user] Question regarding: FASTQ Quality Trimmer

2011-11-28 Thread Daniel Blankenberg
Hi Rahul, This is the maximum number of bases which can have their score not included when calculating the result of the selected aggregation function. For example, if you had a 5 base window with scores of 5,5,2,5 and 5, set aggregation to min score with a specified value of 4, with the

[galaxy-user] Question regarding: FASTQ Quality Trimmer

2011-11-23 Thread Rahul Kanwar
Hello, I am running Galaxy locally and it has been performing flawlessly! I wanted to get more insight about this flag in the FASTQ Quality Trimmer program: Maximum number of bases to exclude from the window during aggregation Does it mean the number of 5' bases to exclude while the doing

[galaxy-user] Question about building a reference genome index using Bowtie

2011-11-10 Thread William Light
I am trying to compare two genetically different strains that I have sequenced using SOLiD. I was trying to ask where these two strains are different, either in terms of deletions or polymorphisms, and one idea I had was to use Bowtie to create an index from one of these strains and then to map

[galaxy-user] Question about file formats

2011-11-10 Thread Rena Zheng
Hi, I uploaded a bed file to Galaxy and did some text manipulations. I want to download the new file as a bed format that I can then open up in excel or a text editor. However, when I save the data, it is a .tabular format that I cannot open with these programs. What should I do? Thanks,

Re: [galaxy-user] Question about file formats

2011-11-10 Thread Peter Cock
On Thu, Nov 10, 2011 at 6:10 PM, Rena Zheng rzh...@mail.med.upenn.edu wrote: Hi, I uploaded a bed file to Galaxy and did some text manipulations.  I want to download the new file as a bed format that I can then open up in excel or a text editor.  However, when I save the data, it is a .tabular

Re: [galaxy-user] question about uploading data through URL method

2011-11-08 Thread Jennifer Jackson
Hello Xaingmimg, When you uncompress the archive locally, does it contain a single file with more than 5000 reads? The consistent results and even number of reads (5000) may mean that the archive contains more than one file. Currently, Galaxy will only load the first file in an archive.

Re: [galaxy-user] question about uploading data through URL method

2011-11-07 Thread Simao Lee
You can download DRA files directly by FTP to Galaxy . . Just paste the FTP address directly in the file box when using upload from my computer Best Simon On 7 November 2011 04:54, Xiangming Ding din...@ucla.edu wrote: Hi galaxy I am a new user of galaxy. i met a problem and didnot find

Re: [galaxy-user] question about uploading data through URL method

2011-11-07 Thread Jennifer Jackson
Hello Xiangmimg, Data files can be loaded using a URL on the Get Data = Upload form. FTP and HTTP connections are supported. This is briefly described on that form. If you are still having issues, there may be a problem with file compression or the connection. Downloading locally then using

Re: [galaxy-user] question about uploading data through URL method

2011-11-07 Thread Xiangming Ding
Hi the file name is spr097786.fastq.bz2.After upload it showed spr097786.fastq. It showed it only contain around 5000 sequence reads. I also tried to upload through FTP. so i download the file to my computer and then upload to FTP in galaxy. the totlal 800M file was uploaded to the FTP

[galaxy-user] question about sorting barcoded sequences

2011-10-17 Thread Qingquan Liu
Hi, I have an Illumina HiSeq lane of sequences, in which I input multiple samples with 5-prime 6 bp barcodes. The barcodes were added in a way so that the barcodes are the first 6 bp in the reads. What I need to do is to sort my reads according to the barcodes, then clip off the barcodes and use

[galaxy-user] Question about formattung mouse (mm9) GTF

2011-10-12 Thread shamsher jagat
I have read in the mailing list that you have a workflow which can modify the human GTF file so that it will be compatible with Top Hat. Will it also work with Ensembl mm9 GTF or there is a different work flow. Thanks ___ The Galaxy User

Re: [galaxy-user] QUESTION

2011-10-06 Thread Jennifer Jackson
Hello, For tools that allow a custom genome, the form will include an option to use a Dataset from the history (or similar). Then a sub-menu will pop up where the reference genome can be selected. Other basics: For the query sequences, Fastq or fasta format may be required. After upload,

Re: [galaxy-user] Question

2011-09-27 Thread Jennifer Jackson
Hello Diana, For the main public Galaxy server, an input sequence file of this size should not be a problem when analyzed through the standard tools. Hard quotas are not set at this time, but will be announced soon. Current guidelines can be found at: http://galaxyproject.org/wiki/Main

Re: [galaxy-user] Question

2011-09-26 Thread Georgios Magklaras
On 09/23/2011 09:26 PM, dtr...@ira.cinvestav.mx wrote: Hi, mi name is Diana Trejo and I am working with galaxy for first time. I would like to analyze millions of sequences in galaxy but I don´t know if it is possible because my file is 330 MB. Are there any MB restriction for using galaxy?

[galaxy-user] Question

2011-09-23 Thread dtrejo
Hi, mi name is Diana Trejo and I am working with galaxy for first time. I would like to analyze millions of sequences in galaxy but I don´t know if it is possible because my file is 330 MB. Are there any MB restriction for using galaxy? Thanks for your help Diana Trejo -- This message has been

[galaxy-user] question about the GATK tools

2011-08-18 Thread Hong, Xiaojing
Hi, I just uploaded the BAM file for an exome sequencing sample and was trying to use the GATK tools. In the first step, realigner Target creator, I can see my uploaded file but I can't see any options under the using reference genome and the following choices so I can't click execute. Did I

Re: [galaxy-user] Question about Cuffdiff

2011-08-04 Thread Jennifer Jackson
Hello Luciano, This was a bug, fixed in galaxy-central yesterday: changeset 4212f675f95b . You can either pull the changeset into your local instance or wait for it to be incorporated into the next distribution (within the next few weeks). Next time, it would be great if you would send

Re: [galaxy-user] question about using bowtie

2011-07-29 Thread Jennifer Jackson
Hello William, The tools in NGS: QC and manipulation, especially those in the sub-section AB-SOLiD data can do the manipulations needed before mapping. It may be helpful to view the screencast at http://usegalaxy.org, center pane, quickie #9. Hopefully this helps to get you started, Best,

[galaxy-user] question about using bowtie

2011-07-28 Thread William Light
I am trying to use bowtie to assign reads to the s. Cerevisiae genome. I have data from paired end SOLiD sequencing with two unique six base pair barcodes. Can I use bowtie to make csfasta and qual files from my mixed original data split by bar code? I know I can use the trim option to remove

Re: [galaxy-user] Question regarding quality filtering of 454 amplicons

2011-07-01 Thread Jennifer Jackson
Hi Jackie, The screencasts under Metagenomic Analyses with Galaxy specifically use 454 data and would likely be helpful, maybe even if you have already resolved your prior issue. http://main.g2.bx.psu.edu/screencast Apologies for the delay in reply, we were a bit backed up with questions in

Re: [galaxy-user] question on cufflinks output

2011-06-27 Thread YBao
Hi galaxy-users When trying to display a set of chip microarray data in UCSC main, , we encounter this error: Error(s): Error line 38879 of http://main.g2.bx.psu.edu/root/display_as?id=3221463display_app=ucscauthz_method=display_at: chromEnd larger than chrom chr21_random size (1679928 1679693)

Re: [galaxy-user] question on cufflinks output

2011-06-27 Thread Jennifer Jackson
Hello, The error is indicating that the end of your dataset is larger than the chromosome it is aligned to for this line (at least). This is expected when attempting display of certain data types at UCSC. This is a known issue. You can either remove these lines from your dataset with tools

Re: [galaxy-user] question on cufflinks output

2011-06-25 Thread Jeremy Goecks
Hello Wen, It's not necessary to send multiple emails to the mailing list; we track incoming emails to ensure that we respond to all of them. Your FPKM values do look high, but keep in mind that coverage is only part of the FPKM calculation; it's also dependent on transcript length and the

[galaxy-user] question on cufflinks output

2011-06-24 Thread Wen Huang
Dear Galaxy team and users, I have a question on the output by cufflinks on Galaxy. I started with about 28M paired-end reads and mapped them to the reference genome using Tophat on Galaxy. The aligned fragments were assembled by cufflinks, again on Galaxy and I got an output with the first

[galaxy-user] Question please -manhattan plots

2011-06-19 Thread Sagi
Dear sir, I was looking through your Galaxy Wiki, but could not find an answer to my question. I would most appreciate any help regarding the following issue: I'm conducting a GWAS study in horses. Up until now I've been using PLINK for my association analysis, and now I wish to generate a

[galaxy-user] Question about output CuffDiff SplicingDiff

2011-06-16 Thread Felix Mayr
Hi there, Looking at the output of the SplicingDiff files of CuffDiff, me and my colleagues are preplexed about the output of the p_values and q_values. We've tried different inputs of different samples to compare but never seem to manage to get p_values smaller than 0.50 and we keep getting

Re: [galaxy-user] Question about output CuffDiff SplicingDiff

2011-06-16 Thread Jeremy Goecks
Felix, You seem to be providing the correct inputs to Cuffdiff and it appears to be producing valid output. More information about setting parameter values and interpreting Cuffdiff can be found in manual: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff Good luck, J. On Jun 16, 2011, at

Re: [galaxy-user] Question about output CuffDiff SplicingDiff

2011-06-16 Thread Rory Kirchner
What version of Cufflinks is your Galaxy installation running? A recent version (1.00 and 1.01) had a problem that was causing the splicing and promoter use tests to have very few differentially regulated genes, according to http://cufflinks.cbcb.umd.edu/. -rory On Jun 16, 2011, at 8:13 AM,

Re: [galaxy-user] question about Filtering Cufflink files

2011-05-09 Thread Jeremy Goecks
Jagat, First, a couple housekeeping issues: (a) the questions you're asking are better suited to the galaxy-user list (questions about using Galaxy and performing analyses) rather than galaxy-dev (questions about installing Galaxy locally and tool development), so I've moved this thread to

[galaxy-user] Question regarding quality filtering of 454 amplicons

2011-03-10 Thread Jackie Lighten
Hi, I have a question for you guys regarding quality filtering. I have a data set of double MID tagged 454 amplicons, from which I wish to select high quality sequences above Q20. The 454 quality filtering system seems to work differently from that given for the Illumina sequencing i.e. 454

Re: [galaxy-user] Question About FTP

2011-02-07 Thread Danny Park
Hey Jennifer, I was using email/password, just tried again and I got in. Weird. Thanks for the quick response! Danny On Mon, Feb 7, 2011 at 3:21 PM, Jennifer Jackson j...@bx.psu.edu wrote: Hello Danny, Are you connecting to main.g2.bx.psu.edu and using your Galaxy credentials