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guigolab / bamstats

A command line tool to compute mapping statistics from a BAM file
BSD 3-Clause "New" or "Revised" License
21 stars 3 forks source link

Output only includes general statistics #33

Open mulderdt opened 7 months ago

mulderdt commented 7 months ago

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 commented 7 months ago

resolved. needed -a annotation.gtf

output now have coverage and rnaseq statistics