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