Entering edit mode
7.6 years ago
praveenhcu131
•
0
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
Which peak caller would you suggest @Devon?
MACS2 is very popular in general. BCP has better sensitivity. MUSIC is more sensitive for broad peaks like h3k4me3.
can you please tell me how to plot the distribution around tss from macs out put files
You wouldn't, you'd plot the read density (make a bigWig file with bamCoverage) and plot that (computeMatrix and then plotHeatmap or plotProfile).
sir can u tell detailed procedure how to do that
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.
i have done plotpca and plot profile from now where i have to measure the breadth of peak
The normal options would be:
i have to measure the width from transcription start site to end site how can i measure it from png image
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.