Output from macs subcommand 'bdgpeakcall'
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12 weeks ago
arsala521 ▴ 10

Hi

I have a TF ChIP-seq wig file from NCBI GEO with the following top few lines:

track type=wiggle_0 name="Bed Format" description="xyz.tagAlign , smoothed, background-subtracted tag density" visibility=dense color=200,100,0 altColor=0,100,200 priority=20
X 5 40 8.01596910471638
X 105 140 9.84274069026994
X 205 240 10.3630144423714

I had to call peaks from this wig file so I converted this wig to bedgraph and used Macs subcommand bdgpeakcall. I got the ten-column output (copying first 3 lines):

track type=narrowPeak name="xyz_peak.bed" description="xyz_peak.bed" nextItemButton=on
chr2L   193     5728    xyz_peak.bed_narrowPeak1  323     .       0       0       0       2585
chr2L   5928    8328   xyz_R1_peak.bed_narrowPeak2  404     .       0       0       0       350

Is the header for this bed narrowpeak file same as it is for ENCODE bed narrowpeak file? The header for ENCODE bednarrow peak file is: chrom; chromStart; chromEnd; name; score; strand; signalValue; pValue; qValue; peak (Point-source called for this peak)

and I am trying to find if columns of Macs narrowpeak output represent same information. Specially for the last column, does it indicate ''Point-source called for this peak".

Thank you

Output macs header • 212 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. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.
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Thanks for editing my post. I tried using code option but it wasn't representing the file content properly. I will try to present my post better next time.

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