quality control rRNA mapping

Question

[ferozef]

Hi, I'm trying to learn how to align my sequencing data to rRNA region so that, I will know the total % of reads maps to rRNA regions. I used STAR aligner to align my raw data (hg19). Can anyone please help me since I'm very new to bioinformatics.

Thanks in advance

Feroze

[gb]

using bedcov en depth from samtools to check the depth and coverage.

Answer 1

[caggtaagtat]

Hi,

I use the tool sortMeRNA for that. It includes rRNA databases and can be used to align your reads to the databases, in order to exclude them from downstream analysis, if thats what your asking for.