Entering edit mode
6.6 years ago
Ron
★
1.2k
Hi all,
I want to quantify variants of genes ,present in a bed file with RNA-seq data. Usually I use STAR (alignment) + Cufflinks (for expression),using gtf file.
Can I convert bed file to gtf,so that I can use Cufflinks to calculate expression? Or is there any way to use bed file itself with Cufflinks?
Here is my BED file :
chrX 66914515 66915917 AR-V7.specific 0 + 66914515 66915917 0 1 1402, 0,
chrX 66763874 66766604 AR.full.exon1 0 + 66763874 66766604 0 1 2730, 0,
Thanks, Ron