Given many genomic coordinates, how do I find those that have matching 5' or 3' ends, regardless of length. for example:
chr1 10 20 feat1 . +
chr1 10 25 feat2 . +
chr1 12 20 feat3 . +
All the features overlap, but I am only interested in feat1 and feat2 which share the same start position, or in this case the 5'. Should I be interested in the 3' end, than, feat1 and feat3 (plus the coordinates).
I have looked at the options of bedtools but couldn't find out how to do this. Is there a tool out there that allows me to do this, if so which, or go I have to cobble something together? I guess awk is always an option.
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A. Domingues
I am only interested in feat1 and feat2
create a pseudo-column [chrom/start] , join the file with itlself, remove the self/self
join -t $'\t' -1 1 -2 1 <(sed 's/\t/_/' input.txt | sort -t $'\t' -k1,1 ) <(sed 's/\t/_/' input.txt | sort -t $'\t' -k1,1 ) | awk -F '\t' '($2!=$6)' | tr "_" "\t"
Nice idea, but the the join does not seem to be working:
join -t $'\t' -1 1 -2 1 <(sed 's/\t/_/' a.bed | sort -t $'\t' -k1,1 ) <(sed 's/\t/_/' a.bed | sort -t $'\t' -k1,1 )
chr1 10 20 feat1 . +
chr1 10 25 feat2 . +
chr1 12 20 feat3 . +
The full command returns nothing.
Works on my machine. what's your delimiter ?
Tabs but these were converted to spaces, so I double checked, and also with "," as a separator, and the problems is awk:
join -t $'\t' -1 1 -2 1 <(sed 's/\t/_/' a.bed | sort -t $'\t' -k1,1 ) <(sed 's/\t/_/' a.bed | sort -t $'\t' -k1,1 )
chr1_10 25 feat2 . + 25 feat2 . +
chr1_100 20 feat1 . + 20 feat1 . +
chr1_12 20 feat3 . + 20 feat3 . +
In this example, the second field is always similar to the sixth and thus awk -F '\t' '($2!=$6)' fails. Anyway, your idea gave me something to work with. Thanks.
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