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featureCounts output

Hi all,

I try to use featureCounts for making count table from the macs2 narrowPeaks files. However, I found that some rows of chr, start, end have repeat value: enter image description here

Do anyone know what is wrong from my output?

Best

macs2 featurecounts
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updated by rfran010 • rfran010 • written by QX • QX

Hi, here is my code (I actually take it from one of your post years ago :))

awk 'OFS="\t" {print $1"."$2+1"."$3, $1, $2+1, $3, "+"}' ${peak_all_dir}peak_all_peaks.narrowPeak > ${peak_all_dir}featureCounts_peaks.saf

featureCounts -a ${peak_all_dir}featureCounts_peaks.saf \
    -F SAF \
    --read2pos 5 \
    -T $SLURM_CPUS_PER_TASK \
    -p \
    -o ${peak_all_dir}featureCounts_peaks_countMatrix.txt ${dedup_dir}*.bam
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written by QX • QX

Do you have any idea why it happens to my count table?

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written by QX • QX

1 answer

Your narrowPeak files has repeated peaks. Usually I think happens due to different summits within peaks or something. There is a MACS2 option to disable this type of output

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written by rfran010 • rfran010

Alternatively, you can filter your peak or SAF file for unique lines. (Can be done with basic command line tools, or bedtools with the peak file).

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written by rfran010 • rfran010

thank you, I will try!

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written by QX • QX

hi @rfran010, can you elaborate more on "different summits within peaks"; why this is the case?

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written by QX • QX

Not sure what type of answer you're interested in, but you can have a region that has multiple peaks that are apparently connected.

Take this random example of ATAC-seq signal, normal behavior will call this as one peak, but you can see three sharp "summits". I believe --call-summits is the relevant option where MACS3 will then re-analyze peaks for summits and instead of calling this as peak1 (red bar) it will report peak1a, peak1b, and peak1c (blue arrows), however each of these will have the exact same chr, start, and end of the red peak. [[please note, this is a random shot from a browser I was looking at. It may or may not be a call-able peak, but either way it illustrates the point]]

See also this post: Why are there duplicate peaks in ENCODE ATAC-seq output?

enter image description here

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written by rfran010 • rfran010

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