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Question: quality control rRNA mapping
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gravatar for ferozef
17 months ago by
ferozef • 20
ferozef • 20 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
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modified 17 months ago by caggtaagtat • 900 • written 17 months ago by ferozef • 20

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

ADD REPLY • link written 17 months ago by gb • 1.2k
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gravatar for caggtaagtat
17 months ago by
caggtaagtat • 900
caggtaagtat • 900 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 COMMENT • link written 17 months ago by caggtaagtat • 900
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