Re: [galaxy-user] FTP upload problem
Hi, I have been having FTP issues for the past several days. I am using Filezilla. The upload starts, then stops after about 32MB and the connection closes and tries to reopen, then closes again. I also tried the command line ftp client in win7 with same results. rich From: Jennifer Jackson To: Fatih Ozsolak Cc: galaxy-user@lists.bx.psu.edu Sent: Tuesday, August 21, 2012 12:51 PM Subject: Re: [galaxy-user] FTP upload problem Hi Faith, There was an FTP issue on our side earlier today, but your processing does not quite fit the usual symptoms. Please try to FTP again using a client that will allow interrupted transfers to be resumed (FileZilla, CyverDuck) see if that helps. You might also want to check your general internet connection - there are several "speedtest" type tools that can detect problems. Use google to locate one or if you have a system administrator they should be able to help. Very sorry to hear that you are having problems but hopefully one of these options will help, Jen Galaxy team On 8/21/12 9:34 AM, Fatih Ozsolak wrote: > Hi, > > I am trying to upload 12 fastq files to Galaxy via FTP. The FTP is > randomly loosing connection, caussing interruption of the upload. Can > you let me know what is wrong? > > Thanks, > fatih > > > ___ > 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://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/___ 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] cuff... errors
Hi, Ive been trying to run cufflinks/cuffdiff but keep getting this error: Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. is there a system issue or something with my data? r ___ 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] ftp
Hi, Is anyone else having trouble connecting to main.g2.bx.psu.edu for FTP uploads? I cannot seem to connect since yesterday. Rich ___ 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] ILLumina 1.9 Hiseq
I have a question about the groomer. Do all Illumina runs need to be groomed, or are there situations where it can be skipped?? (My data says illumina 1.5, so ive been picking input type as illumina 1.3-1.5.) rich From: Jennifer Jackson To: Ateequr Rehman Cc: "galaxy-user@lists.bx.psu.edu" Sent: Wednesday, February 29, 2012 10:57 AM Subject: Re: [galaxy-user] ILLumina 1.9 Hiseq Hello, The input quality score type should be set as "Sanger" for your data. Thanks! Jen Galaxy team On 2/29/12 7:39 AM, Ateequr Rehman wrote: > Dear Glaxy users and admin > > I ran my sequence data on FASTQC tool, > output says it is > Encoding Sanger / Illumina 1.9 > > now i want to groom my file, but groomer does not have option for 1.9 in > "Input FASTQ quality scores type" > > any idea which option i should select to grroom my file, > > later i want to run Bowtie or Tophat, > > Thanks > ** > > > > ___ > 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/wiki/Support ___ 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] downloading (and renaming) output files from Galaxy public server
Hi, I have generated a transcript file using cufflinks for the human (hg19) or zebrafish(zv9) assemblies. When I try to display the cufflinks "assembled transcripts" in UCSC I get this error in the UCSC browser and it wont display the transcripts. human: GFF/GTF group NM_005638 on chrX+, this line is on chrY+, all group members must be on same seq and strand zebrafish: "GFF/GTF group vapb on chr6+, this line is on chr7-, all group members must be on same seq and strand" Any ideas? Rich___ 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] is public galaxy down?
I am unable to access for past several hours. Are others having the same issue? rich ___ 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] tar.gz files
Hi, My seq core returns FASTQ files to me in *.txt.tar.gz format. When I upload this to galaxy, it unzips, but it is apparently still TAR'd and cannot be read. Is it possible to upload this format, or do I need to untar and unzip it first (which is less than ideal)? Rich ___ 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] disk quota not updating
yup...took a while, but eventually resolved. thanks. rich From: Nate Coraor To: Richard Mark White Cc: Jennifer Jackson ; "galaxy-u...@bx.psu.edu" Sent: Monday, December 5, 2011 3:39 PM Subject: Re: [galaxy-user] disk quota not updating On Nov 30, 2011, at 12:49 PM, Richard Mark White wrote: > Hi, > I was nearing my disk quota (at 97%), so I deleted a large number of >datasets using "delete permanently". But my usage did not go down at all. Is >there a delay in this happening, or is there some way to purge the files? Hi Richard, It can take a bit if you delete a large amount of data at once. Did your usage eventually decrease? --nate > > richard > > ___ > 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] public interface issues
Likewise. I can get to my "Saved Histories", but when i click on one, very few items (if any) show up in the rightside panel. ive also tried multiple browsers, etc. rich From: Cittaro Davide To: "galaxy-u...@bx.psu.edu" Sent: Monday, December 5, 2011 7:39 AM Subject: [galaxy-user] public interface issues Hi all, I can't use the public interface in an effective way: items in history (i.e. the green boxes) cannot be expanded. More important, names of the items remind me something that has to deal with the tool/library path (e.g. 2010_03/pilot2/README_pilot2_snps). This happens on OS X and MS Windows systems, Firefox and Safari. Thanks d /* Davide Cittaro, PhD Head of Bioinformatics Core Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute Via Olgettina 58 20132 Milano Italy Office: +39 02 26439140 Mail: cittaro.dav...@hsr.it Skype: daweonline */ ___ 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] disk quota not updating
Hi, Thanks for the info and I did what you suggested. But still no luck. I deleted everything, and when I add up the data totals in my active histories (I have nothing shared) it adds up to 376gb, but i am showing 100%. any ideas? rich From: Jennifer Jackson To: Richard Mark White ; "galaxy-u...@bx.psu.edu" Cc: closetic...@galaxyproject.org Sent: Wednesday, November 30, 2011 1:09 PM Subject: disk quota not updating Hi Richard, Yes, it takes a short time for the UI counts to update. If you deleted permanently, then the result should be what you expected. Should the quota count remain high by tomorrow, that would point to an issue with lingering data counting in the quota. Places to search for unexplained disk use: 1 - Older pre-quota "deleted" datasets that were not permanently deleted. You can check for these in the View Histories -> advanced -> deleted set. The far right column "Status" will note deleted vs permanently deleted. 2 - Shared histories can count towards a quota. So, if not needed or only portions are, copy out of these what you want to use and ask the user that shared the data to "unshared" you, so you don't get stuck with the entire history in your quota. Shared histories/data and quotas are somewhat tricky to tune, and better solutions may be developed as the details are worked out, but this is the current implementation. A good feature to know about is that an imported dataset from a public Data Library never counts towards your quota (if left unmodified). You have probably seen this, but for others who may be reading the thread, this wiki has many details and tips for managing data: http://galaxyproject.org/wiki/Learn/Managing%20Datasets One last comment - it would be very helpful for us if questions were sent with the mailing list as a "to" recipient, so that our ticket tracker picks it up. Hopefully this helps! And please feel free to ask if you need more help or the disk size is not what you expect after the counts refresh. Best, Jen Galaxy team On 11/30/11 9:49 AM, Richard Mark White wrote: > Hi, > I was nearing my disk quota (at 97%), so I deleted a large number of > datasets using "delete permanently". But my usage did not go down at > all. Is there a delay in this happening, or is there some way to purge > the files? > > richard > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support___ 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] disk quota not updating
Hi, I was nearing my disk quota (at 97%), so I deleted a large number of datasets using "delete permanently". But my usage did not go down at all. Is there a delay in this happening, or is there some way to purge the files? richard ___ 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] downloading (and renaming) output files from Galaxy public server
Hi, I am using the galaxy public server. Is there a way to access output files (via ftp, perhaps) so I can bulk download them to my computer? I am over my quota and want to get data off of Galaxy but prefer not to do this all one at a time. Similarly, is there a way to access a directory (via unix, ftp, etc) to rename files quickly while they are on Galaxy, since renaming each output file (i.e. the multiple ones output from cuffdiff) within galaxy is very inefficient and time consuming. Thanks. Rich___ 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] fastq groomer
Hi, So, I am getting a fastq groomer error on some illumina data, with the following error. any ideas? There was an error reading your input file. Your input file is likely malformed. It is suggested that you double-check your original input file for errors -- helpful information for this purpose has been provided below. However, if you think that you have encountered an actual error with this tool, please do tell us by using the bug reporting mechanism. The reported error is: 'Invalid fastq header: lab/solexa_public/Zon/111021_WICMT-SOLEXA_64KF7AAXX/QualityScore/s_3_1_sequence.txt rich From: Jennifer Jackson To: arabidopsis Cc: galaxy-user@lists.bx.psu.edu Sent: Wednesday, November 2, 2011 9:19 AM Subject: Re: [galaxy-user] fastq groomer Hello Slon, In case you are still having issues, the best use case for Illumina 1.8+ data is to run the FASTQ Groomer tool with the option "Sanger". As Peter noted, this assigns the expected datatype plus verifies content before investing time in downstream analysis. Please let us know if more help is needed, Best, Jen Galaxy team On 10/18/11 1:02 AM, arabidopsis wrote: > Hi all, > > Fastq groomer has Solexa or Illumina 1.3+ as an input quality format. I > asked at the sequencing facility about their machine and output and they > said their format was Illumina 1.8+ (the newest). I tried to convert my > fastq file into Sanger by fastq groomer, using Illumina 1.3+ as an input > option and got all reads with quality of around 10... Does it mean that > Galaxy cannot be used on a dataset with 1.8+ encoding or something else > was wrong? > > Thanks, > > Slon > > > ___ > 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/wiki/Support ___ 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] permanently delete problem
actually, i just waited a bit and now they are deletd. r From: Nate Coraor To: Richard Mark White Cc: GANDRILLON OLIVIER ; "galaxy-u...@bx.psu.edu" Sent: Wednesday, October 26, 2011 12:55 PM Subject: Re: permanently delete problem Richard Mark White wrote: > hi, > so i went to options-->saved history-->advanced-->deleted datasets. then > checked all of them, and then hit "permanently delete". > but nothign happened. they still show up as deleted, and they are taking up > lots of my quota. > how do i get rid of these? > > rich Hi Rich, I'm not sure what's going on here, I'm looking in to it. --nate___ 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] permanently delete problem
hi, so i went to options-->saved history-->advanced-->deleted datasets. then checked all of them, and then hit "permanently delete". but nothign happened. they still show up as deleted, and they are taking up lots of my quota. how do i get rid of these? rich ___ 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] 1000 genome variant calls
i've been using a tool called annovar for this. it is a perl script, but on a mac or linux box very easy to implement (via terminal window on mac). will filter based on dnSNP, 1000 genomes or complete genomics datasets. very straightforward with really no programming ability needed. rich From: Jennifer Jackson To: galaxy-user ; svem...@uthsc.edu Sent: Tuesday, October 4, 2011 9:24 PM Subject: [galaxy-user] 1000 genome variant calls Repost Original Message, Please send all replies to "all" Hello Jennifer, I am a new to Linux and have no programming skills and hence galaxy is the only rescuer for me. I have nextgen dna seq data. I finished analysis and now have a list of variants. I want to see if these variants are already in 1000 genome data released in Aug 2011. I want to upload list of my chromosome locations and see if they are any matches with 1000 genome data. IS there a way we can do it in galaxy...instead of writing scripts to do it. Like I said, I have no programming skills. Thanks. ___ 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/
[galaxy-user] TopHat--BAM merge
Hi, I mapped two illumina runs using TopHat (they are from same RNA sample). Then tried to use the BAM merge tool to make this into one BAM file for further processes. But it returned an empty file. Is this not possible? Maybe I am not understanding the purpose/use of BAM merge? Rich ___ 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] zero vs 1 based
Hi, This must seem like a newbie question but I cant get a clear answer. My understanding from the galaxy wiki page http://wiki.g2.bx.psu.edu/Learn/FAQ#Learn.2BAC8-FAQ.Interval_and_BED_format is that all intervals in galaxy are 0 based, start inclusive end exclusive. but when i use generate pileup/filter pileup and convert to intervals, i get something like this: chr10 1056309 1056310 G C + When i look up the SNP (G-->C) it is pretty clearly 1056310. Which would make the "interval" end inclusive. this is key because when i annotate snp's against dbSNP, i need to have the right cooridnates. Can anyone provide some guidance? Thanks! rich___ 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] Trimming small RNA
Hi, This must seem like a newbie question but I cant get a clear answer. My understanding from the galaxy wiki page http://wiki.g2.bx.psu.edu/Learn/FAQ#Learn.2BAC8-FAQ.Interval_and_BED_format is that all intervals in galaxy are 0 based, start inclusive end exclusive. but when i use generate pileup/filter pileup and convert to intervals, i get something like this: chr10 1056309 1056310 G C + When i look up the SNP (G-->C) it is pretty clearly 1056310. Which would make the "interval" end inclusive. this is key because when i annotate snp's against dbSNP, i need to have the right cooridnates. Can anyone provide some guidance? Thanks! rich ___ 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] rna-seq mutation detection
Hi, Thanks very much. I've tried this, but one thing I have noticed is that if I do the initial mapping with BWA vs. Bowtie the # of variants I get is much larger with BWA. I have seen mention on the web that you need to change the quality score annotation for BWA before running SAMtools, but not sure precisely how to do this. any thoughts? Rich From: Jeremy Goecks To: Richard Mark White Cc: "galaxy-user@lists.bx.psu.edu" Sent: Sunday, August 28, 2011 2:18 PM Subject: Re: [galaxy-user] rna-seq mutation detection Rich, Given that you're analyzing your RNA-seq data using Galaxy, I'd guess that you're using Tophat to map your reads onto on reference genome. If this is the case, then you can use the BAM files produced by Tophat to generate variation data for each sample. The variation tools that you'll want to look at are [NGS: SAM Tools-->]Generate Pileup [NGS: GATK Tools-->]Unified Genotyper (only avaiable on our test server and still in beta) The outputs for each tool produce a consensus base for each potential variation site, and you can compare the consensus base for each sample to look for differences. If you're doing de novo assembly of your RNA-seq data to look for variation, you'll need to use tools that are not currently available in Galaxy. Good luck, J. On Aug 18, 2011, at 12:22 PM, Richard Mark White wrote: Hi, > I am trying to look at differences between two RNA-seq samples to see if >there are mutations in one of them relative to the other (i.e. not in >comparison to a reference genome). Does anyone know of a way to do this >within galaxy? Any help is appreciated! > > >rich > >___ >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/
[galaxy-user] rna-seq mutation detection
Hi, I am trying to look at differences between two RNA-seq samples to see if there are mutations in one of them relative to the other (i.e. not in comparison to a reference genome). Does anyone know of a way to do this within galaxy? Any help is appreciated! rich ___ 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] rna-seq CDS, splicing and TSS fails
Hi all, So I am using cuffdiff to find significant differences between two samples (no replicates). The transcript and gene differential expression works and I get significant values. However, consistently, the TSS, CDS, and splicing differences return with "1 line" and no data. I have tried multiple different GTF transcriptome reference files - UCSC refflat, ensembl, but still no luck. Maybe I am missing something very basic - can anyone give me advice here? Richard ___ 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] wiggle file
Hi, this should be simple but it is not..forgive the newbie question. i am doing chip-seq. bowtie>sam filter for mapped reads>MACS. i want to create a wiggle file that displays in ucsc, but when i choose the "WIG" option on macs, and then try to show it in UCSC, it treats each line of the created WIG file as a separate track, and obviously does not show it as a graph. is there a wiki page somewhere that can give me the basics? or can someone point me in the right direction? thanks. rich___ 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/
