Error with bigWigAverageOverBed

Question

[María José]

Hi,

I'm trying to calculate average coverage from narrowPeak files, using bigWigAverageOverBed command. However, I get the following error:

bigWigAverageOverBed coverage_u1.bw u1.narrowPeak average_u1.txt 

invalid unsigned integer: "type=narrowPeak"

I'm following a guideline from someone who has done this process before. However, I haven’t been able to find any resources addressing this specific error.

Any insight or resources would be greatly appreciated

Answer 1

[ATpoint]

It chokes because there is a header line in the narrowPeak file that needs to be removed. The tool expects a BED file which is at minimum chr-start-end without any headers. Transform your narrowPeak file in that way. At simplest it is just skipping the first line sed "1d" < your.narrowPeak > your.bed-

Answer 2

[Pierre Lindenbaum]

check the formats of your u1.narrowPeak and average_u1.txt they're most proably NOT bed file.

show us the output of

head u1.narrowPeak average_u1.txt | tr "\t" "%"