How to get specific genes in bed format where each exon is covered base by base?

Question

[MAPK]

I have MAP2K1, JAK1, JAK2 and few other genes. I want to get the exonic regions of these genes in bed format base by base (i.e including every base in the table and not in the range format).

[Devon Ryan]

Like "samtools depth -b regions.bed ..."?

Answer 1

[venu]

First you need to look at this thread.

After getting exonic coordinates for every Gene use samtools faidx to get the sequence of that range. Will be done with simple bash scripting.