% of transcriptome covered

[Yasmin]

Hi,

Just came across this very useful group! I hope you can send me in the right direction.

My question is: after running STAR (2 pass) on my rna-seq data, I would like to know what is the % of the reference transcriptome that was covered.

Can you point me to where in the output files I can gather this info?

Many thanks,

Yasmin

[Alexander Dobin]

Hi Yasmin,

STAR does not make this calculation, you would have to do post-mapping analysis, which will depend on how you define the transcriptome coverage.

For instance, you can collapse all annotated exons into "exonic" intervals, and calculates their coverage using bedtools.

Cheers

Alex