Output only includes general statistics

[mulderdt]

Hello,

Can you clarify how to generate the rnaseq statistics using bamstats? The readme says the following:
"Provided statistics
Bamstats can currently compute the following mapping statistics:
general
genome coverage
RNA-seq"

But when I run it on my STAR genome aligned or bowtie2 transcriptome aligned bams I only get general statistics. Is it using some information in the bam header to determine whether it is an rnaseq experiment?

Is it related to the -a parameter? I am unclear as to what that does as well.

Running the following code:

bamstats -i F137214.Aligned.out.sorted.bam -o F137214_stats.json

Thanks

[mulderdt]

resolved. needed
-a annotation.gtf

output now have coverage and rnaseq statistics