Hi guys and girls,
One of my coworkers is scrambling to redo a figure for a manuscript under review. The reviewers want to see a graphical representation of the number of reads from an RNA seq experiment. My coworkers is a biologists and computers are not his strong suit. We received a BAM file from the company who did the sequeuncing. However, they are not very responsive about getting us the data needed for the figure. I am probably the most computer literate in the lab, but I have never dealt with next-gen sequencing data, so I ma completely at a loss.
From some of the other questions on the forum, I gathered that Samtools could to this. We are interested in plotting the number of reads in "Chr2: 212,000,000 – 213,800,000". I assume, you would do some kind of sliding window in order to bin the reads?
Any pointers would be greatly appreciated!
EDIT: thanks for all the help. Each of the proposed options seems to come with its own little problems. I am sure I'll figure it out though!