Unknown chromosome results in .narrowPeak files

Question

[StacyG]

I've run macs2 callpeaks and in the .narrowPeak file I have many rows for chromosomes with names like "chrUn_KI270522v1". Can anyone tell me what this means? The peak was found in an unknown chromosome? Is this due to noise and can be ignored? I have a feeling if I ignore those rows I'm going to be missing out on important info but I get many errors when I try to annotate the peaks because those aren't real chromosomes.

Any insight would be appreciatd.

FYI - These are human cells.

Thanks

Answer 1

[ATpoint]

This is normal and expected unless you filter these contigs out before peak calling (I always do). It's unplaced contigs.

See for example: https://gatk.broadinstitute.org/hc/en-us/articles/360035890951-Human-genome-reference-builds-GRCh38-or-hg38-b37-hg19

[StacyG]

Thank you! Can you tell me how to filter out these contigs? I'm new to all of this so sorry if this is a basic question

[ATpoint]

From the BAM file (alignment) or the peak file?

[StacyG]

I guess the .bam files since you said you filter them out before finding the peaks. That makes more sense to me.

[StacyG]

I figured out how to use bamtools filter to get chr1 but is there a way to give it a list of the chromosomes I want and remove the contigs that are a problem? Thanks

[ATpoint]

I usually use samtools. Given a sorted and indexed file you can do:

Extracting the primary chromosomes from the BAM header, this will eliminate everything like chrU, *_random etc:

samtools idxstats $bam | cut -f1 | grep chr[1-9,X,Y] | grep -v '*' | xargs samtools view -o filtered.bam $bam

Or just manually, listing the chromosomes to keep:

samtools view -o filtered.bam $bam chr1 chr2 chr3 ...

[StacyG]

Thanks so much