[pbluescript]

Originally Posted by NicoBxl

is this bedtools command correct ?


intersectBed -abam alignment.bam -b coordinates.gff > alignment_filtered.bam

Thanks,

N.

EDIT > I found it : intersectBed -abam alignment.bam -b coordinates.gff -wa > alignment_filtered.bam

The GFF format and bed format have the genomic coordinates in different columns, so you will have to fix that first.