Question: quality control rRNA mapping
0
gravatar for ferozef
2.2 years 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 • 424 views
ADD COMMENTlink modified 2.2 years ago by caggtaagtat1.3k • written 2.2 years ago by ferozef20

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

ADD REPLYlink written 2.2 years ago by gb1.9k
0
gravatar for caggtaagtat
2.2 years ago by
caggtaagtat1.3k
caggtaagtat1.3k 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 2.2 years ago by caggtaagtat1.3k
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