Question: Why ranges of narrowPeak file and that of bed file are not identical
0
gravatar for Wang
11 months ago by
Wang10
Wang10 wrote:

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
..
sequencing chip-seq macs2 • 535 views
ADD COMMENTlink modified 11 months ago by ATpoint34k • written 11 months ago by Wang10

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.
code_formatting

ADD REPLYlink written 11 months ago by RamRS27k

ok,I got it!.thank you!

ADD REPLYlink written 11 months ago by Wang10

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
ADD REPLYlink modified 11 months ago by RamRS27k • written 11 months ago by Wang10

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.

ADD REPLYlink written 11 months ago by genomax83k

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

ADD REPLYlink written 11 months ago by Wang10
1
gravatar for ATpoint
11 months ago by
ATpoint34k
Germany
ATpoint34k wrote:

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.

ADD COMMENTlink written 11 months ago by ATpoint34k

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

ADD REPLYlink written 11 months ago by Wang10

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

ADD REPLYlink modified 11 months ago • written 11 months ago by ATpoint34k

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

ADD REPLYlink written 11 months ago by Wang10
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