extract alignment from SAM with a GFF file

[NicoBxl]

Hi,

All is in the title. I aligned small reads (~25nt) with bowtie on my reference genome and I've a GFF file with annotations.

Is it possible to extract only the alignment that are in the gff file ?

Thanks,

N.

[colindaven]

Bedtools or Galaxy should do it! Extract the SAM alignments according to the GFF coordinates.

R would also be an option.

[NicoBxl]

how can I do that with R ?

[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

[pbluescript]

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.