Retrieve coordinate for maximum value in a region using a bigwig file
Hello,
I have a bed file with a series of regions and a signal bigwig file. I want to look for each region in the bed file what is the maximum value in the bigwig file, and then obtain the genomic coordinated for the maxima. I have seen ways to get the maximum, but not how to get a coordinate position. Any leads?
Thanks!
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Pierre Lindenbaum
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written
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am2622 •
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written
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am2622 •
1 answer
A one-liner (not tested)
echo -e "chr1\t1014511\t1023256\nchr1\t1014570\t1014600" | while read CHROM START END ; do echo -en "${CHROM}\t${START}\t${END}\t" && bigWigToBedGraph -chrom=${CHROM} -start=${START} -end=${END}path/to/file.bigWig stdout | sort -t $'\t' -k4,4gr | head -n 1 |tr -d "\n" && echo ; done
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