I went through the RNAseq workflow (I didn't do Cuffmerge) and from the
Cuffdiff output gene and transcript differential expression testing I filtered
some data. For example, for two samples I got about 400 gene and 900 transcript
differential expressed with fold change >2. Since I am working with a fungus
whose genome annotation is in a format (gff) not accepted by Cuffmerge or
Cuffcompare in Galaxy (the accepted one is GTF2), the Cuffdiff output tells me
only the position of relevant genes on the scaffolds.
Going to genome browser and see which gene is in that position is fine for few
genes, but doing that for all 400 or 900 is something probably impossible.
Does anybody have a helpful suggestion on what I can do? It would be great if
there was a program where based on the position of the genes on the scaffold
(Cuffdiff output) I can get their information using the annotation file. I have
also the gene annotation file in gene bank format (gbk) but I don't see a way
to use it for what I need.
Giuseppe Ianiri, Ph.D.
Division of Cell Biology and Biophysics
School of Biological Sciences
5100 Rockhill Road
University of Missouri-Kansas City
Kansas City, MO 64110
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