Question: Cuffdiff Without Gene Annotation
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Ianiri, Giuseppe • 90 wrote:
Hello guys,
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.
Thanks
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
Email: ianirig@umkc.edu