Bedtools and BEDOPS closest/closest-features issues
I have a bed file with hg19 motif coordinates that I would like to annotate. I downloaded the hg19 refFlat bed file from UCSC and (after sorting both files with the sort function) tried to use the closest function in bedtools to annotate the closest gene. However, I my output only shows the following:
MBP:manual_annotations$ bedtools closest -a sorted.abcd.bed -b sorted.refFlat.bed -d
chr19 940789549407959 E-box-116519 --box-11+805 chr1
934341 935552 HES4 0 934438 935353 0 4 471,88,96,307, 0,564,730,904, 769
chr19 940789549407959 E-box-116519 --box-11+805 chr1
934343 935552 HES4 0 934438 935353 0 3 469,88,481, 0,562,728, 769
closest-features in BEDOPS gives me a similar output.
Adding the > to a file just outputs my motif file in its entirety.
Any ideas on what's going on?
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can you show
head -2 sorted.abcd.bed sorted.refFlat.bedare they sorted ?Hey thanks - the file wasn't sorted because the motif bed file was in the MAC text format. I used HOMER's changeNewLine.pl utility to change to UNIX format, sorted and then used closest and it worked. Now I have each peak annotated twice for some reason but working on that:)
Edit: The duplicate gene names are different isoforms.