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:
File2.gtf, first 5 rows:
I ran
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
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:
Code:
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";
Code:
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";
Code:
intersectBed -a File2.gtf -b File1.gtf -wa -wb -f 1.0 -s -r > overlap_newSegments_internal
Any idea why this might be? Is intersectBed sensitive to the order in the files?
Thanks,
Boel
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