Question: weird problem with summit.bed file from macs2
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gravatar for mikysyc2016
17 months ago by
mikysyc201660
mikysyc201660 wrote:

Hi all, I just find my bed file after using macs2 is not common(all the end - start equal to 1). But other files as narrow.peak and excel file are common. And bedgraph is also common( can see clear peak in IGV). summint.bed: chr1 3127206 3127207 ppar_2.72_peak_1 2.44687 chr1 3141438 3141439 ppar_2.72_peak_2 5.84966 chr1 3603620 3603621 ppar_2.72_peak_3 5.34279 ....... narrow peaks: chr1 3127019 3127287 ppar_ko1_2.72_peak_1 24 . 4.17374 5.25954 2.44687 187 chr1 3141408 3141611 ppar_ko1_2.72_peak_2 58 . 6.87514 10.28014 5.84966 30 chr1 3603509 3603773 ppar_ko1_2.72_peak_3 53 . 6.26061 9.49989 5.34279 111

this is the command i used: $ macs2 callpeak -t '/home//Desktop/FGC1867_s_4_CGATGT.bt2.sorted.bl.bam' -c '/home/Desktop/FGC1867_s_4_TTAGGC.bt2.sorted.bl.bam' -f BAM -g mm --bdg -n ppar_2.72 -q 0.01 --outdir ppar2_0.01_q

Can you give me some suggestion? Thanks a lot!

ADD COMMENTlink modified 17 months ago by jared.andrews073.9k • written 17 months ago by mikysyc201660

It is a summit bed, so i think it is the right type. And narrowpeak is a bed file not just give peak summit. I think that will be the reason. Is it right?

ADD REPLYlink written 17 months ago by mikysyc201660
0
gravatar for jared.andrews07
17 months ago by
jared.andrews073.9k
St. Louis, MO
jared.andrews073.9k wrote:

The summits file is just that - the summit of each peak. It's showing the position (base) for each peak that has the highest signal. That's what they're supposed to look like.

ADD COMMENTlink written 17 months ago by jared.andrews073.9k
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