Question: quality control rRNA mapping
0
gravatar for ferozef
17 months ago by
ferozef20
ferozef20 wrote:

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

rna-seq • 329 views
ADD COMMENTlink modified 17 months ago by caggtaagtat900 • written 17 months ago by ferozef20

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

ADD REPLYlink written 17 months ago by gb1.2k
0
gravatar for caggtaagtat
17 months ago by
caggtaagtat900
caggtaagtat900 wrote:

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.

ADD COMMENTlink written 17 months ago by caggtaagtat900
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