home/knowledge/showKnowledge/sig/ucsc-bigwigaverageoverbed

[utterances-bot]

bigWigAverageOverBed manual with usage examples | BioQueue Encyclopedia

bigWigAverageOverBed - Averaging scores in a bigWig file for the regions/intervals given in a bed file. BioQueue Encyclopedia provides details on the parameters, options, and curated usage examples for bigWigAverageOverBed.

https://open.bioqueue.org/home/knowledge/showKnowledge/sig/ucsc-bigwigaverageoverbed

[2202next]

bigWigAverageOverBed in.bigWig in.bed out.tab
the output is：0 duplicated in input bed and nothing else

[2202next]

Does anyone know what is wrong?

[bioq-comm]

You probably have duplicated records in your input bed file. You can use the following commands to get unique records and feed them into this command:

sort -k1,1 -k2,2n input.bed | uniq > input.uniq.bed

[2202next]

You probably have duplicated records in your input bed file. You can use the following commands to get unique records and feed them into this command:

sort -k1,1 -k2,2n input.bed | uniq > input.uniq.bed

Thanks for your reply, the reason for the error is indeed that there is a column in my bed file with the same value.

[regenerativescience]

bigWigAverageOverBed in.bw promoters.bed out.tsv returns invalid unsigned integer: "-423"

promoters.bed was created as follows.

wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.annotation.gtf.gz
gunzip gencode.v43.annotation.gtf.gz
mv gencode.v43.annotation.gtf annotation.gtf
awk '{if($3 == "gene") {
        gsub(/\"/, "", $14);
        gsub(/;/, "", $14);
        print $1 "\t" $4-1000 "\t" $4+1000 "\t" $14
    }}' annotation.gtf > promoters.bed

I would be grateful for your time and would appreciate your advice on how to deal with this.

[bioq-comm]

BED files should not have negative values for start or end positions. Your command for creating promoters.bed can result in negative values if $4 (the start position) is less than 1000. You can either use bedClip to remove these invalid regions or modify your awk command to handle cases where the start position is less than 1000 (e.g. setting starts as 0)

[regenerativescience]

@bioq-comm
I apologise for any inconvenience caused by my oversight. I have resolved the issue based on the advice you kindly provided. Thank you very much for your guidance and support.