Dear Biostars
Does any one how to overlap stand-specific paired-end RNA-Seq reads (BAM) with known protein coding genes (BED) ?
I tried the following but I think it is not the correct way ? Would appreciate your help!
bamTobed -i ES.bam > ES.bed
intersectBed -a ES.bed -b Ensembl_mm9.bed -wa -s |awk '!a[$4]++' |wc -l