Hi all! I am trying to get ChIP-seq peaks from ENCODE ChIP-seq data. The particular experiment I am interested in is GSM613815. When I download the .bed files from GEO, however, I get a lines that look like this:
chr1 9859 10058 SOLEXA5_123:3:23:15452:1914
Unfortunately, this does not have scores, names, strands, etc according to the .bed file format, like so:
chr1 91852645 91853203 SRX005383.05_peak_1 612 . 17.40168 67.74557 61.27857 379
How would I use the information in the first file to get peaks I can use (second line)? Is it a conversion or do I have to do anything else?
•
written
by
lkalesin •
2 answers
I think what you have there is simply the sequencing reads in BED format, even though note that this is not standard BED because strand would need to be in column6 instead of column5. To make a proper BED file, do something like:
awk 'OFS="\t" {print $1, $2, $3, $4, ".", $5}' in.bed > out.bed
This file you could use to call peak e.g. with macs2 -t out.bed -f BED.
I don't think you downloaded the peaks, as ATpoint mentioned, these are probably bed files of reads ("TagAlign"). The peaks from ENCODE are usually supplied in .narrowPeak files. Maybe try the roadmap website for downloading the peaks (it's subheader "C. peak calling", make sure to scroll down).
Log in to answer this question.
-
bedtools genomecov issue with calculating coverage across called peaks?
written by lescano.v.jr •
-
ChIP-seq Peak calling from BED or WIG file
written by gspirito •
-
How to get probe-specific intensity values including genomic positions from microarray ChIP-chip da…
written by Marcel •
-
Understanding columns of ChIP-Seq BED file format
written by singram •
-
ENCODE Chip-seq Data Format
written by Shicheng Guo
-
Methylation levels at specific sites
written by firatuyulur
-
How to obtain peak height values from a bed file?
written by morovatunc
-
RNA-seq bed format read by pash3.0
written by jesselee516
-
Remove Blacklist regions from ChIP-seq Data
written by Ulduz •
-
Loading Large Bed Files Into Bioconductor
written by danielcook2013 •
