Hi Biostars community,

I have bam files with RNA-seq results from ~1000 of single cell samples. For every transcript in each sample, I would like to calculate what percentage of spliced transcript's length is covered by aligned reads. Besides, It would be great to have this value for coding part of transcripts only, or, ideally, for every exon.

What would be the most straightforward way to do this?

Thanks a lot!
Thanks to WouterDeCoster and Bastien Herve for their answers!

I have found out that bedtools does exactly what I need:

bedtools coverage -hist -abam "your bam file" -b "your bed file" > "file with results"