Question: Where to find reference gene model for C. elegans to compute FPKM using RseQC?
0
gravatar for s.singh
4 weeks ago by
s.singh20
University of California, United States
s.singh20 wrote:

Hi,

I am trying to do a raw read count (FPKM) for my RNAseq data using RseQC. The data I have is of C.elegans and I am not sure where to find its "Reference gene model bed file". RseQC is not accepting GTF/GFF file.

Can you suggest other tools which can find FPKM for my RNAseq data?

Thanks -S

rseqc next-gen rnaseq • 75 views
ADD COMMENTlink written 4 weeks ago by s.singh20
1

Did you try the recommendation from the RSeQC manual?

BED file for other species and the most recent release of these files can be downloaded from UCSC Table Browser

ADD REPLYlink written 4 weeks ago by h.mon30k

Hey, Thanks so much for pointing to this. I somehow had missed this. I didn't know that there was such thing as "Table Browser" available on UCSC.

Thanks a lot!

-S

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by s.singh20
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