Why ranges of narrowPeak file and that of bed file are not identical
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2.6 years ago
Wang ▴ 10

Hi everyone!

I did peak call using MACS2 to analysis a Chip-seq data and I found the ranges in the narrowPeak file is not same as that in the bed file.what dose this mean?and why?Thanks!

more ff_peaks.narrowPeak

chr1    3044565 3044674 ff_peak_1       97      .       3.97001 12.89295        9.76606 21
chr1    3050086 3050252 ff_peak_2       332     .       13.90061        38.02962        33.29285        77
chr1    3050434 3050592 ff_peak_3       91      .       6.33852 12.18861        9.14707 69
..

 

more ff_summits.bed 

chr1    3044586 3044587 ff_peak_1       9.76606
chr1    3050163 3050164 ff_peak_2       33.29285
chr1    3050503 3050504 ff_peak_3       9.14707
..
ChIP-Seq MACS2 sequencing • 1.6k views
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Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
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ok,I got it!.thank you!

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I run macs2 this way

macs2 callpeak -t ff.bam -c input.bam -n ff -f BAM -g mm

ff.bam and input.bam was sorted by samtools

samtools sort -@ 32 1.bam  >ff.bam
samtools sort -@ 32 2.bam  >input.bam
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Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep the threads logically organized. SUBMIT ANSWER is for new answers to original questions.

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Sorry! I'm newbie here. Maybe I should edit the original post and append these informations.

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2.6 years ago
ATpoint 57k

The narrowPeak file contains the entire interval of the peak, the ff_summits.bed the peak summits so the base with the highest read pipeup.

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Thank you,I really appreciate it! Is there any detailed materials or article I can read? I failed to find these information in the official README.md

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Check the data format definitions at UCSC and the macs documentation, the latter explicitely explains the outputs.

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OK,thank you.May be I missed some useful information.I'll read these again.

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I have been using narrowPeak files for downstream analysis (annotation, motif finding, differential peak calling), should I use the summits.bed or narrowPeak files?

I'm asking this because narrowPeak files have many peaks start-end ranges if use --call-summits in MACS2. So I only keep 1 unique peak as the entire interval of the peak and plot Venn diagram among samples. The number will be different when I use summits.bed because it has more lines (1 peak with multiple sub-summit intervals).

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Hello, have you got any answer for your question from any different source? When I try to visualize overlapping peaks with the summits.bed results do not seem good

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