Where to find reference gene model for C. elegans to compute FPKM using RseQC?

Question

[s.singh]

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

[h.mon]

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

[s.singh]

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