March 2011 - galaxy-user - lists.galaxyproject.org

Re: [galaxy-user] [galaxy-bugs] Cufflinks issue
by Jeremy Goecks 03 Mar '11

03 Mar '11

Brandon, > I tried replying to the galaxy userlist but it said its for authorized users only, and i asked for permission but no response yet. You can manage your subscription to galaxy-user here: http://lists.bx.psu.edu/listinfo/galaxy-user/ > I just had one quick question, the output files from of CDS diff, promoters diff and splicing diff from cuffdiff only report have sqrt(JS), teststat, and p value stats? Correct. You can find full details of Cuffdiff's outputs in the manual: http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff_output J.

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Re: [galaxy-user] [galaxy-bugs] Cufflinks issue
by Jeremy Goecks 02 Mar '11

02 Mar '11

Brandon, These type of questions--questions about to use Galaxy--are best directed to the galaxy-user list, so I've moved it there. > I saw this thread, though it is older I just want to make sure I did my > analysis after the update. > > http://www.mail-archive.com/galaxy-user@lists.bx.psu.edu/msg00084.html > > You mention having to repeatedly merge cufflinks output for cuffcompare to > generate the combined transcripts. I was able to add them all in the > cuffcompare section with the "add new Additional GTF input file". also my > command is: > > > > cuffcompare -o cc_output -r > /galaxy/main_database/files/002/048/dataset_2048606.dat -R -s > /galaxy/data/hg19/sam_index/hg19.fa ./input1 ./input2 ./input3 ./input4 > ./input5 ./input6 ./input7 ./input8 ./input9 ./input10 > This is correct: Galaxy now supports an arbitrary number of input files to cuffcompare, making repeated merging unnecessary. > Also I was reading on seqanswers that cuffdiff didn't work with biological > replicates > > http://seqanswers.com/forums/archive/index.php/t-7905.html, but when I did > my galaxy analysis it had the "perform replicate analysis" available and was > wondering if you had an updated version or did something else. I am > analyzing a control and diseased group, with 5 biological samples in each > group. Cuffdiff should work fine on this right? I got FPKM as output. > Also do you know what statistical methods cuffdiff is using for analysis? > Cuffdiff claims to support biological replicates, and, as you found, Galaxy provides the infrastructure to specify replicates to Cuffdiff. I do not know the statistical methods used for analysis, but this would be a good question to ask either on seqanswers or on the new tophat-cufflinks mailing list: tophat.cufflinks(a)gmail.com > Lastly, in cuffdiff, the CDS, promoters and splicing analyses didn't seem > to work (datasets 190,191,192). any ideas? > This is because the p_id attribute is not being attached to the combined_transcripts dataset produced by Cuffcompare. This problem is due to your reference file being incorrect -- it should be dataset 81, your reference annotation. Thanks, J.

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Re: [galaxy-user] Extract sequences from [gtf file] + [genome FASTA file]
by Jeremy Goecks 02 Mar '11

02 Mar '11

Dinesh, Please send questions such as these to the galaxy-user mailing list (which I've cc'd). You can find the 'Extract Genomic DNA' tool under the 'Fetch Sequences' menu. You may also want to use tool search ('Options -> Show Tool Search'). Thanks, J. On Wed, Mar 2, 2011 at 2:31 PM, <dinesh(a)gwu.edu> wrote: > Hi Jeremy, > You have asked to extract only the exons using the 'Extract Features' > tool but all I see here in my developer version under 'Extract Features' is > 'Gene BED To Exon/Intron/Codon BED expander'. But the cufflinks files is a > gtf file... I have tried to use the above tool but it returns an empty file. > Do I need to convert my gtf to bed and then extract the exons and then use > the 'Extract Genomic DNA' tool? > > Thank You > Dinesh Cyanam > George Washington University > >

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Re: [galaxy-user] how to find out the gene_ID correspond to CUFF ID
by Jeremy Goecks 02 Mar '11

02 Mar '11

(cc'ing galaxy-user) Sorry Jeremy, I'm being a bit dense here - where exactly are these tools in > the tool list - I can't find them... David, Both tools are located within the 'Operate on Genomic Intervals' menu. Also, remember that tool search (Options -> Show Tool Search) is useful for finding a tool. Best, J.

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how to find out the gene_ID correspond to CUFF ID
by Ying Zhang 01 Mar '11

01 Mar '11

Dear Everyone: I have got one output file after I run Cufflink which contain gene expression information. However, I found out for each gene_ID, it has the format like, CUFF.1151175, do you have idea of how to find out the offical gene ID correspond to this CUFF ID? Thank you very much! Best Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286

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Re: [galaxy-user] Problems using aaChanges tool
by Jennifer Jackson 01 Mar '11

01 Mar '11

Hello Vasu, Are you still have problems? Updating to the most current distribution dated Feb 18th would be advised, as a starting point: hg pull -u -r ca0c4ad2bb39 https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBriefs Please give this a go and let us know if there continue to be issues with using the save icon on your local instance. Best, Jen Galaxy team On 2/17/11 6:52 AM, vasu punj wrote: > > I had problem in the past saving sam file from Galaxy's floppy sign and > at that time Jen mentioned there was a bug which was fixed. After a > month or so I cannot save the file. Any one has any suggestion please. I > am running Galaxy on local server. > Thanks. > > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

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