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Question: zero cuffdiff FPKM values SusScrofa
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gravatar for dutartas
3.6 years ago by
dutartas • 0
Czech Republic
dutartas • 0 wrote:

Good morning,

I am a beginner in RNAseq Galaxy interface and I have a problem with all zero FPKM values in cuffdiff output. I used SusScr3 build in genome for tophat alignment and SusScrofa 10.2.gtf from UCSC for cuffdiff. How can I check if these two files are compatible? Where I can download gtf.file compatible to SusScr3 build in genome?

Thank you for all answers

Martin
cufflinks • 1.1k views
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modified 3.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.6 years ago by dutartas • 0
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gravatar for Jennifer Hillman Jackson
3.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If the reference annotation file (GTF in this case), was obtained from UCSC, then this is a match for the susSrc3 reference genome. Double checking the sequence identifiers won't hurt, but I expect that this is a match already.

The issue instead is likely the content of the GTF file itself - specifically the attributes assigned when these files are extracted from the Table Browser. While useful for many analysis, the GTF version of the extracted data is not the best fit for the Tuxedo pipeline - it is missing attributes that are necessary for full Cuffdiff statistic generation. As an alternative, try the version from iGenomes. These are specially formatted for this tool set.

Best, Jen, Galaxy team
 
ADD COMMENT • link written 3.6 years ago by Jennifer Hillman Jackson ♦ 25k
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