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!
The link to your example doesn't appear to be working.
But see the question Converting Bam To Bedgraph For Viewing On Ucsc? for some possibly helpful ideas.