We have sequenced some targeted regions and mapped reads (36bp) to whole reference genome (hg18). I have a bed file which have coordinates of captured regions. I want to see (plot), what is the distribution of reads mapped to my captured regions relative to 100bp up and 100bp down to captured regions. Example - I have 10,000 regions captured but I mapped reads to whole genome. All captured regions have different length and I want to calculate relative value for all the regions so that I can make a nice plot. If I have a region, say,
chr1 153 400
Now I want to see, how many reads are mapped to 153-100 i:e from 53 to 153 and 400+100 i:e from 400 to 500 and of course from 153 to 400. So I have 3 read depth values. I want to do it for all captured regions. I can calculate this for all regions using bedtools coverageBed but in the end, I have to plot the relative values to show how reads are distributed from 100 bp upstream of captured regions, then captured regions and then 100bp downstream of captured regions.
Any suggestions? How would you do it?
Thanks and Best regards,