Groseq data read count?

Question

[ahsan.raza.rana]

I have just seen that: 1. read counts actually shows the coverage. 2. groseq bedgraph last column is the coverage means read count.

I dont know read counts are coverage or there is any way to count the reads. Am I right or wrong? Please guide me. Its urgent

Hi, I have to find the read count of Groseq datathat are also in an other file which is chipseq data. How can i find it? Should i use bedtool with -c option to find groseq count? or there is a separate way to find the read count from groseq data?

An important thing is that i have only bedgraph and bed file of groseq.

Kindly guide me i urgently need help

[GouthamAtla]

As your question is not clear, I assume that you want to see if the GRO-Seq data overlaps with Chip-Seq peaks.

As you have only bedGraph file, you could use clusterBed to make windows of overlapping regions, and then use groupBy to sum up the coverage in those windows, such that at the end you have a bed file with different windows and the coverage for those windows, which you could overlap with chip-seq data. Its a bit tricky, hope you got some idea.

[Devon Ryan]

Please elaborate a bit on what you mean by "read count of Groseq data that's also in another file." It might be best to just state what the biological question you're trying to answer is, since you likely don't need to do what you're trying to do.