Using Bed File With Cuffdiff To Determine Expression Of Specific List Of Genes.

Question

[nepalis]

Hi,

I have a list of genes in bed format. I need to determine the expression levels of this genes in the experiment. I have aligned the file using tophat and i have cufflinks results too from older runs. Is there a way to determine the expression level for the genes in the bed format for tophat alignment and cufflinks output ? Is converting the bed file to gtf file and rerunning the rnaseq pipeline again only way ?

thanks!

Answer 1

[Devon Ryan]

It's a bit unusual to have genes in bed format, but I suppose that could be used. If you had the genes in GTF or GFF format, the normal reply would be to simply use htseq-count, but that won't work with your bed file. Your best bet is to load the bed file into R and create a GRangesList from it. Then you can open your SAM/BAM files and use countOverlaps to get per-gene counts. I suspect that creating a properly formatted GRangesList from a BED file will prove non-trivial, but it should be doable.