Calculate Tag density

Question

[Picoskia]

Hi everyone,

I was wondering how to calculate the density over a specific list of genes. Which file should i use to start this analysis and how do i count the tags? I have MACS2 output file, is there a column in those file where tag count is specified for each of the peaks?

Thank you for your kind help :-)

[venu]

The details are not sufficient to suggest a workflow or tool. You could try to explain in detail what your goal is.

That being said, if you have a bed file with gene coordinates and BAM file, there are number of tools to calculate raw read/tag density and normalized read density. E.g. deeptools, bedtools, featureCounts...etc. The MACS2 output file contains coordinates for the regions where the antibody that has been ChIP'd potentially binds. So basically you can annotate these regions to nearest genes by bedtools intersect function to see which genes are enriched for the ChIP.

[Picoskia]

I would like to plot the tag density for a certain group of genes. For this i need the tag count as well as the normalised read density as you said.

I have looked to different tools but haven't found where to get the tag count information

[venu]

May be you have to look up definition of tag count one more time. Check this: ChIP seq basic terminology: what is a ChIP-seq tag?

plot the tag density for a certain group of genes

What do you mean by plotting? If you want to visualise ChIP enrichment over some genes, you can use IGV or pyGenomeTracks.

[Picoskia]

i just want the tag/read numbers