BigWig format (Cut&Run)
1
0
Entering edit mode
21 months ago
Usama • 0

I generated summit.bed files from my experiment cut&run, and I followed the below steps to get and visualize the bigwig files. 1) I used awk to get a bedgraph:

awk '{printf "%s\t%d\t%d\t%2.3f\n" , $1,$2,$3,$5}' myBed.bed > myFile.bedgraph

2) Sorting the bed files:

sort -k1,1 -k2,2n myFile.bedgraph > myFile_sorted.bedgraph

3) Chrom.size:

samtools faidx genome.fasta 
cut -f1,2 genome.fasta.fai > genome.size

4) I used the UCSC bedGraphToBigWig tool:

bedGraphToBigWig myFile_sorted.bedgraph myChrom.sizes myBigWig.bw

The problem:

I encountered a problem with the visualization in IgV; the bigwigs look a bit weird. The bigwig didn't show nicely peak-like bumps of signals, but shows narrow, rectangular towers as if it's just marking summits or the presence/absence of a peak instead of the different heights along the peak interval.

I followed exactly the above mentioned steps (sorted, created the chrom file and converted to bigwig) Cut&run data, hg38). Could it be that there is some other parameter that I should add that I am ignoring?

How to visualize the bigwig files instead of IgV??

Thank you

BigWig • 1.0k views
ADD COMMENT
3
Entering edit mode
21 months ago
ATpoint 85k

A summit BED file is just a file with a single coordinate interval per peak. A bedGraph has a fourth column for the coverage over a region but for this you need the alignment (bam) files. You cannot convert a summit file to a bedGraph. Use something like bedtools genomecov or deeptools bamCoverage to get bedGraphs/bigwigs.

ADD COMMENT
0
Entering edit mode

Thank you very much for your suggestion. My question is I have used MACS2 to get the peaks, the output files of macs2 are: -sample.lambda.bdg -sample_treat_pileup.bdg -sample_peaks.xls -sample_peaks.narrowPeak -sample_summit.bed

I used the previous codes on summit.bed to get bigwig files, is it correct? or I have to change to _pileup.bdg??

Note: the analysis for Cut&Run experiment.

ADD REPLY

Login before adding your answer.

Traffic: 1601 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6