I am working on RNA SEQ data for pombe genome. I mapped the reads with the pombe genome and created sam/bam files.
Now my question is i have a list of pombe genes with its coordinates.
I want to find the number of read counts for those genes.
How can i do that. Any code would be really helpful.
I will explain a bit more.
Suppose my gene coordinate for gene SPAC227.11c is 567876 568100
Now i want to find the read coordinates for the gene SPAC227.11c.
How should i do it.
Hope to hear from you guys soon