gappedPeak format MACS2

Question

[boczniak767]

HI, I need some clarification of gappedPeak format (said to be 12+3 BED format) produced by MACS2 link to program. So, taking one row from such file we have:

• 1 [chromosome]
• 33763 [broad region start]
• 35412 [broad region end]
• hds6q10_peak_3 [peak name]
• 19 [10*-log10qvalue, grey level for graphing purposes]
• . [strand]
• 33763 [start of the first narrow peak in the region] - this and next value are the same as 2nd and 3rd column, respectively (in my case in every row???!)
• 35412 [end of the first narrow peak in the region]
• 0 [RGB color key]
• 3 [how many blocks including the starting 1bp and ending 1bp of broad regions]
• 1,258,1 [the length of each block]
• 0,709,1648 [starts of each block]
• 3.51331 [fold change]
• 4.48131 [-log10pvalue]
• 1.99450 [-log10qvalue]

I don't fully understand the data in columns for which I used bolded description. For example, why for the length of each block there are ones? I suppose it's not because peak is 1nt long.

Also, it should be possible to use the file in the UCSC browser, it is not the case however (at least in genomaize version of that link). Changing strand "." to "+" not helps

Answer 1

[dfournie]

I have the impression that length of each block gives you the length of the "gap". For instance on a H3K27me3 i have a peak somewhere with value: 1,349,1 Which corresponds on the browser track as the size of the gap. Surrounding peak size may not matter, so they give just value 1. I'm just guessing.