Question about wheat RNAseq

[sahusarika]

Hello all
I hv done reference based assembly of wheat rna seq dataand used bowtie for alignment and mapping. I hv used cuffdiff for DGE and in the result I hv got gene ID of wheat like Trea_4B....
Pls help for the annotation.... How to do?
How to determine the coverage ratio of RNAseq data?

[Gordona]

If you knew what version release you used as your reference genome that would help find the annotation to go with it. For example on Ensembl Plants you can download GFF3 files for version 31:
ftp://ftp.ensemblgenomes.org/pub/pla...ticum_aestivum

http://plants.ensembl.org/Triticum_aestivum/Info/Index

I don't know what you mean by coverage ratio, perhaps someone else can help..
Best wishes