Question: zero cuffdiff FPKM values SusScrofa
gravatar for dutartas
3.6 years ago by
Czech Republic
dutartas0 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


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ADD COMMENTlink modified 3.6 years ago by Jennifer Hillman Jackson25k • written 3.6 years ago by dutartas0
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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 COMMENTlink written 3.6 years ago by Jennifer Hillman Jackson25k
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