Awesome! Thank you :)
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bedtools merge with strandedness giving now output
Hello, I have a bed file and need to merge with strand specificity, but I am not getting an output. My command is:
bedtools merge -i input.bed -s > merged.bed
My bed file looks like :
chr1 65702 65714 +
chr1 71879 71891 -
chr1 97442 97454 -
chr1 97552 97564 -
chr1 125938 125950 +
chr1 134489 134501 -
chr1 165663 165675 -
chr1 173419 173431 +
chr1 176257 176269 +
chr1 176263 176275 +
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1 answer
Try this:
awk '{OFS="\t"; print $1,$2,$3,".",".",$4}' INPUT.bed | bedtools merge -i - -s
Bed format contains strand information in column 6.
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