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chipseq data analysis

how to calculate the h3k4me3 breadth in chipseq data it is oe of the feature which i want to study please tell me how to calculate the peak breadth

chip-seq r
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updated by Biostar Biostar • written by praveenhcu131 • praveenhcu131

1 answer

You have two options:

  1. Call peaks and determine the widths from the BED file.
  2. Forget peaks and plot the distribution around the TSS. You'll see a large peak there, so just measure the width.
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written by Devon Ryan Devon Ryan

Which peak caller would you suggest @Devon?

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written by Deepak Tanwar Deepak Tanwar

MACS2 is very popular in general. BCP has better sensitivity. MUSIC is more sensitive for broad peaks like h3k4me3.

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written by Petr Ponomarenko Petr Ponomarenko

can you please tell me how to plot the distribution around tss from macs out put files

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written by praveenhcu131 • praveenhcu131

You wouldn't, you'd plot the read density (make a bigWig file with bamCoverage) and plot that (computeMatrix and then plotHeatmap or plotProfile).

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written by Devon Ryan Devon Ryan

sir can u tell detailed procedure how to do that

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written by praveenhcu131 • praveenhcu131

I already mentioned the exact tools (they're all part of deepTools). You can even do that in Galaxy if you prefer. The deepTools documentation is fairly decent.

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written by Devon Ryan Devon Ryan

i have done plotpca and plot profile from now where i have to measure the breadth of peak

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written by praveenhcu131 • praveenhcu131

The normal options would be:

  • Eye ball it
  • Use photoshop to measure the width
  • Use a ruler
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written by Devon Ryan Devon Ryan

i have to measure the width from transcription start site to end site how can i measure it from png image

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written by praveenhcu131 • praveenhcu131

If your peak is over the whole gene body then you can't get that information from plotProfile, you'll need to get it from your BED/GTF file. I presumed that you had some enrichment in the promoter or around the TSS, whose width you could just approximate by eye.

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written by Devon Ryan Devon Ryan

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