Post Alignment basic QC of RNA-Seq data

Question

[daewowo]

I am trying to find a simple way to generate (post alignment) 1) coverage of reference, 2) depth of coverage - either average or running value accross the genome.

I tried GATK DepthOfCoverage but cant work out the --interval parameter.

samtools bamstats gives coverage

Bases mapped: 1,085,991 (97.8%)

Is there a simple tool that can calculate average depth of coverage and eg min depth max depth

Answer 1

[swbarnes2]

You probably want the percentage of reads assigned to genes. Average coverage would be a silly statistic to work out for RNASeq.