Question: Why ranges of narrowPeak file and that of bed file are not identical
0
gravatar for Wang
16 days ago by
Wang0
Wang0 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 • 129 views
ADD COMMENTlink modified 16 days ago by ATpoint17k • written 16 days ago by Wang0

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 16 days ago by RamRS22k

ok,I got it!.thank you!

ADD REPLYlink written 16 days ago by Wang0

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 16 days ago by RamRS22k • written 16 days ago by Wang0

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 16 days ago by genomax68k

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

ADD REPLYlink written 16 days ago by Wang0
1
gravatar for ATpoint
16 days ago by
ATpoint17k
Germany
ATpoint17k 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 16 days ago by ATpoint17k

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 16 days ago by Wang0

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

ADD REPLYlink modified 15 days ago • written 15 days ago by ATpoint17k

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

ADD REPLYlink written 15 days ago by Wang0
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