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Old 08-28-2012, 08:23 AM   #1
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Location: Auckland, New Zealand

Join Date: Jun 2012
Posts: 6
Default intersectBed (BEDtools) generating empty output file

I have used the Bedtools command intersectBed to check the overlapping between the two bed files. A is my INDEL file and B is my Reference file. But it is producing empty output file. I thought the problem was that the file B is much larger than file A. But I tried with changing the file order still its not creating any output.

Here is the reference B file (larger):

gff_seqname 0 1395 gene 0 +
gff_seqname 0 1395 exon 0 +
gff_seqname 1397 2498 gene 0 +
gff_seqname 1397 2498 exon 0 +
gff_seqname 2524 3619 gene 0 +

Here is my A file with just 51 INDELS:

CHROMOSOME 174708 174713 -GCCGG:2/6
CHROMOSOME 1078686 1078686 +A:105/112
CHROMOSOME 1229123 1229125 -CT:800/870
CHROMOSOME 1234830 1234830 +AT:134/134
CHROMOSOME 1234833 1234834 -A:134/134

here is my command:

intersectBed -a raw.bed -b sodalis_galaxy.bed -wa -wb >test13.bed
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Old 08-28-2012, 08:36 AM   #2
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Location: Auckland, New Zealand

Join Date: Jun 2012
Posts: 6

I can see the chromosome in column 1 doesn't match..!!
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