View Single Post
Old 08-02-2011, 02:45 PM   #5
pbluescript
Senior Member
 
Location: Boston

Join Date: Nov 2009
Posts: 224
Default

Quote:
Originally Posted by NicoBxl View Post
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.
pbluescript is offline   Reply With Quote