bedCons

Given a BED6 file with genomic regions, and a bigWig file with some genomic signal, this program calculates mean, median, and percent of bins with greater than minscore signal over the given regions.

Install

Download the binary and make it executable:

wget https://github.com/jakevc/bedCons/blob/master/bedCons
chmod +x bedCons
./bedCons -h
Usage of bedCons:
  -bedfile string
    	BED6 format file with regions to summarize wig signal over
  -bigwig string
    	big wig file
  -binsize int
    	bin size to summarize bigwig values over (default 50)
  -minscore float
    	the output column percentgt calcualtes the percentage of bigWig bins greater than or equal to this score (default 0.5)
  -outfile string
    	output filename

Example

Some example bedfile with regions from the human genome:

head data/hg38_n_boundaries.bed
chr1	955000	967500	hg38_n_B00012	0.624106357531	.
chr1	1307500	1340000	hg38_n_B00040	0.448953308449	.
chr1	1515000	1527500	hg38_n_B00056	0.629629903428	.
chr1	1695000	1740000	hg38_n_B00067	0.109148377678	.
chr1	1915000	1925000	hg38_n_B00084	-0.582895935256	.
chr1	2175000	2185000	hg38_n_B00109	0.132596293231	.

Summarize phyloP score over these regions:

./bedCons -bigwig hg38.phyloP100way.bw -bedfile hg38_n_boundaries.bed -minscore 0.6 -outfile test.bed

head test.bed
chrom	start	end	name	score	strand	mean	median	percentgt
chr1	955000	967500	hg38_n_B00012	0	.	0.314180	-0.368830	0.232000
chr1	1307500	1340000	hg38_n_B00040	0	.	0.193881	-0.321280	0.215385
chr1	1515000	1527500	hg38_n_B00056	0	.	0.028473	-0.358220	0.128000
chr1	1695000	1740000	hg38_n_B00067	0	.	NaN	-0.130650	0.126667
chr1	1915000	1925000	hg38_n_B00084	0	.	-0.359669	-0.531190	0.130000
chr1	2175000	2185000	hg38_n_B00109	0	.	-0.040980	-0.164530	0.055000
chr1	2415000	2515000	hg38_n_B00132	0	.	-0.531748	-0.732310	0.068000
chr1	3015000	3025000	hg38_n_B00154	0	.	-0.070420	-0.334660	0.120000
chr1	3435000	3445000	hg38_n_B00190	0	.	0.113821	-0.250460	0.185000