extract alignment from SAM with a GFF file

NicoBxl · 08-01-2011, 01:51 AM

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 · 08-01-2011, 05:03 AM

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

R would also be an option.

NicoBxl · 08-01-2011, 05:04 AM

how can I do that with R ?

NicoBxl · 08-02-2011, 01:15 AM

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 · 08-02-2011, 02:45 PM

Quote:

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.

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08-01-2011, 01:51 AM	#1
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	extract alignment from SAM with a GFF file 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.

08-02-2011, 01:15 AM	#4
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	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 Last edited by NicoBxl; 08-02-2011 at 05:47 AM.

08-01-2011, 05:03 AM	#2
colindaven Senior Member Location: Germany Join Date: Oct 2008 Posts: 415	Bedtools or Galaxy should do it! Extract the SAM alignments according to the GFF coordinates. R would also be an option.

08-01-2011, 05:04 AM	#3
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	how can I do that with R ?