intersectBed gives empty file

[Boel]

Hi All,

Stumbled on a strange error when running intersectBed (BEDtools) on two samples that I know are partially overlapping. Here are the first five rows of the two files:

File1.gtf, first 5 rows:

chr1	bed2gff	exon	4541	4636	0.0	*	.	 gene_id "chr1:4540-4636_1"; transcript_id "chr1:4540-4636_1"; exon_number "1";
chr1	bed2gff	exon	4640	4692	15.0	-	.	 gene_id "chr1:4639-6522_1"; transcript_id "chr1:4639-6522_1"; exon_number "1";
chr1	bed2gff	exon	4793	4901	15.0	-	.	 gene_id "chr1:4639-6522_1"; transcript_id "chr1:4639-6522_1"; exon_number "2";
chr1	bed2gff	exon	6470	6522	15.0	-	.	 gene_id "chr1:4639-6522_1"; transcript_id "chr1:4639-6522_1"; exon_number "3";
chr1	bed2gff	exon	4640	4692	8.0	-	.	 gene_id "chr1:4639-6522_2"; transcript_id "chr1:4639-6522_2"; exon_number "1";

File2.gtf, first 5 rows:

chr1	bed2gff	exon	4541	4636	0.0	*	.	 gene_id "chr1:4540-4636"; transcript_id "chr1:4540-4636"; exon_number "1";
chr1	bed2gff	exon	4640	4692	0.0	-	.	 gene_id "chr1:4639-6522"; transcript_id "chr1:4639-6522"; exon_number "1";
chr1	bed2gff	exon	4793	4901	0.0	-	.	 gene_id "chr1:4639-6522"; transcript_id "chr1:4639-6522"; exon_number "2";
chr1	bed2gff	exon	5610	5810	0.0	-	.	 gene_id "chr1:4639-6522"; transcript_id "chr1:4639-6522"; exon_number "3";
chr1	bed2gff	exon	5864	5890	0.0	-	.	 gene_id "chr1:4639-6522"; transcript_id "chr1:4639-6522"; exon_number "4";

I ran

intersectBed -a File2.gtf -b File1.gtf -wa -wb -f 1.0 -s -r  > overlap_newSegments_internal

and end up with an empty result file.

Any idea why this might be? Is intersectBed sensitive to the order in the files?

Thanks,
Boel

[epigen]

What version are you using? I copied your examples and it worked with v2.10.0:

chr1	bed2gff	exon	4541	4636	0.0	*	.	 gene_id "chr1:4540-4636"; transcript_id "chr1:4540-4636"; exon_number "1";	chr1	bed2gff	exon	4541	4636	0.0	*	.	 gene_id "chr1:4540-4636_1"; transcript_id "chr1:4540-4636_1"; exon_number "1";
chr1	bed2gff	exon	4640	4692	0.0	-	.	 gene_id "chr1:4639-6522"; transcript_id "chr1:4639-6522"; exon_number "1";	chr1	bed2gff	exon	4640	4692	15.0	-	.	 gene_id "chr1:4639-6522_1"; transcript_id "chr1:4639-6522_1"; exon_number "1";
chr1	bed2gff	exon	4640	4692	0.0	-	.	 gene_id "chr1:4639-6522"; transcript_id "chr1:4639-6522"; exon_number "1";	chr1	bed2gff	exon	4640	4692	8.0	-	.	 gene_id "chr1:4639-6522_2"; transcript_id "chr1:4639-6522_2"; exon_number "1";
chr1	bed2gff	exon	4793	4901	0.0	-	.	 gene_id "chr1:4639-6522"; transcript_id "chr1:4639-6522"; exon_number "2";	chr1	bed2gff	exon	4793	4901	15.0	-	.	 gene_id "chr1:4639-6522_1"; transcript_id "chr1:4639-6522_1"; exon_number "2";

[Boel]

Yes there is nothing wrong with my files, and I was using an up to data version of BEDtools. But! The second file was HUGE, and the command worked when I changed the order of the files. So problems solved now.