Cuff diff result looks weird

Question

[Bioblazer]

I used cufflinks- cuffdiff to run Differential gene expression analysis, I got the diff expression list some of the FPKM are mentioned for more than one gene What could be possible reason to happen? what is remedy to solve this kind of issue.

XLOC_005229 XLOC_005229 AFLA_041640,AFLA_041650,AFLA_041660 EQ963476:913034-921641 AT30 CI30 OK 2.97088 112.688 5.24529 3.44972 0.00025 0.0441917 yes

Answer 1

[andrew.j.skelton73]

When calculating expression, Cuffdiff utilises a "window" like approach, where a locus is chosen (I've never found out how it chooses the window), and this is given an XLOC code for quantification. This approach can encompass more than one gene and it's an internal mechanism of CuffDiff, not something you can readily change. You can certainly look at alternative approaches to differential gene expression, such as Alignment -> HTSeq_Count -> DESeq2

[Bioblazer]

Thank you for reply. I am already using HTSeq count-> NOISeq, but I just want to know whether any solution to above problem.