[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

[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 tri

[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 ___

Re: [galaxy-user] rna-seq mutation detection

tools, 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, Gi

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

[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 generat

[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

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

[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 _

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 W

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 purp

[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 (vi

[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 ___

Re: [galaxy-user] disk quota not updating

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 shou

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 A

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 No

[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 ___

[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 rep

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+, thi

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

[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 publi

[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 ___

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