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Old 09-04-2012, 06:57 AM   #1
ccard28
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Location: Rhode Island

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Default Galaxy Cuffdiff Values

Hello All,
I am using Galaxy to run Tophat/Cufflinks/Cuffdiff but am running in to some trouble with cufflinks and cuffdiff. I am getting different FPKM values on my cufflinks output of 2 samples when compared to the 2 values that cuffdiff is using from the same two tophat alignments. I have seen a thread on this before but no definitive solution was come to other than maybe the version of cufflinks being used. Galaxy says Cufflinks(version 0.0.5) which compared to the previous thread about this topic seems to be a very old version (if this is a comparable label to cufflinks versions in general and not a galaxy specific label of some sort). Would this presumably be the cause of my differing FPKM values for cufflinks and cuffdiff? Are there any other possibilities? Should I look at working with these analyses in command line based approaches instead of galaxy to solve my problem? I am not very familiar with command line so I was hoping to get this problem solved through galaxy if that is at all possible. If anyone has any suggestions they would be much appreciated. Thank you in advance for any responses.
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Old 09-05-2012, 06:52 AM   #2
ccard28
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Default

Correction, the version of cufflinks and cuffdiff being used is 1.3.0 for both. Previous posts have stayed going to this version have solved problems for people getting different values from cuffdiff and cufflinks but I am still getting different values from the two outputs. Are there any other possible explanations for cufflinks and cuffdiff showing different FPKM values from the two samples?
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