Thanks for the reply. I tried to use the script provided on a previous galaxy thread for adding the chr on to the gtf file on the mac terminal but I keep getting this error -
awk: can't open file ensembl.gtf source line number 1 I am very new to using the terminal so please let me know if there is something basic that I am not doing right, Thanks! Kurinji On Tue, Jun 28, 2011 at 6:13 AM, Jeremy Goecks <jeremy.goe...@emory.edu>wrote: > Hello Kurinji, > > I was at your USC Galaxy seminar last week, which I found very helpful - > thank you! > > > Glad to hear that you found the workshop helpful. As a reminder, please > email questions about using Galaxy and its tools to the galaxy-user mailing > list (which I've cc'd). You may get quicker and different responses from > community members, and everyone will benefit from the discussion. > > I used my recently generated RNAseq data in Galaxy (which was pre-aligned > using tophat and already had cufflinks run on it) - I ran cuffcompare with > all the gtf files and then cuffdiff for the three pairs (there is 1 control > and 3 different drug treatments - no replicates). I got several output > files, as expected, but decided just to look at the gene differential > expression as a start. Some questions I have are - > > 1. (very basic question!) which is sample 1 (and corresponding value 1) and > sample 2 (and corresponding value 2)in my output file. This is what my > output file is called - > > 90: Cuffdiff on data 37, data 38, and data 60: gene differential expression > testing 33,969 lines > > Is 37 sample one or sample two? Given the data - I would expect sample 37 > to correspond to "value 2" - but I could be wrong. Please let me know! > > > The best way to figure out which dataset corresponds with Cuffdiff's labels > is to click the rerun button in the dataset: sample names correspond > directly to the reads datasets (i.e. BAM files) provided as input to > Cuffdiff. > > 2. How do I find the UCSC gene names corresponding with start/end sites - I > did input the hg18 UCSC gtf file as a reference > > > You'll need to use a reference annotation (GTF file) that has the gene_name > attribute as input for Cufflinks/compare/difff. Typically Ensembl > annotations have this attribute; however, you'll need to prepend 'chr' to > each line--really, to each chromosome name--in order to bring Ensembl > notation in line with UCSC/Galaxy notation. > > Actually, I noticed that value 1 in this particular output file is all 0 - > no idea why. It is not this way in the other files, making me wonder if > there is an error somewhere. I am sure the bam file is okay as I viewed it > on IGV and saw the patterns I would expect for some candidate genes I looked > at. > > > It's difficult for me to comment without seeing your analysis. Some output > files depend on particular attributes being set correctly in the annotation > file. You may want to search through our mailing list archives and see if > your question has already been answered: > http://gmod.827538.n3.nabble.com/Galaxy-Users-f815892.html > > Good luck, > J. >
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