How to split the .bigWig file into equal size of bin?
I am trying to output a .bedgraph like the following:
chrom start end mean
chr1 554300 554400 34
chr1 554400 554500 43
chr1 554500 554600 45
chr1 554600 554700 65
chr1 554700 554800 34
from a .bigWig file. how can i do this?
• 1,548 views
•
link
updated
by
Alex Reynolds
•
written
by
solarchan7 •
•
written
by
solarchan7 •
2 answers
use the UCSC tool bigWigAverageOverBed (not tested)
• 0 views
•
link
written
by
Pierre Lindenbaum
Here's another way that lets you control more parameters:
$ assembly=hg38
$ bin_size=100
$ bigWigToWig signal.bw signal.wig
$ wig2bed < signal.wig > signal.bed
$ fetchChromSizes ${assembly} \
| grep -v '_*_' \
| awk -v FS="\t" -v OFS="\t" '{ print $1, "0", $2 }' \
| sort-bed - \
| bedops --split ${bin_size} - \
| bedmap --echo --mean --delim '\t' - signal.bed \
> answer.bg
The bedmap tool will let you swap out --mean with various other statistical operations, for instance (median, max, min, etc.).
• 0 views
•
link
written
by
Alex Reynolds
Log in to answer this question.
More posts like this
-
cufflinks GTF files incompatible with cuffmerge?
written by sahilbioinf0 •
-
Mapping reads from a BAM file to a custom BED file.
written by Shaurya Jauhari •
-
Adding ggplot2 chromosome position variable
written by rbronste
-
Segmentation fault from wigToBigWig when using the -clip option
written by bowensamigger •
-
bedGraph compress tools
written by marina.v.yurieva
-
Error when uploading Wig file to UCSC
written by tamadomi •
-
Memory leak while reading a bigwig in python
written by Geparada
-
bigwig to wig conversion, getting bedgraph
written by mehran.karimzade
-
bigwig to wig conversion
written by jmack159 •
-
How To Extract Scores From Wigfix Files
written by dustar1986
