How do I decide the mapping quality score in featureCounts?
0
0
Entering edit mode
15 months ago
dark.lord ▴ 30

Hey guys,

I noticed that with featureCounts the -Q (quality) makes a big difference. I tried with no -Q (default = 0) and -Q 10, and the results were pretty different:

Q 10

Geneid  Chr     Start   End     Strand  Length  sorted_mapped_3_rRNA.bam
PROKKA_00001    Bin3_16S        1       1533    +       1533    610692
PROKKA_00002    Bin2_16S        1       1533    +       1533    182
PROKKA_00003    Bin1_16S        1       1533    +       1533    4111

Q 0

Geneid  Chr     Start   End     Strand  Length  sorted_mapped_3_rRNA.bam
PROKKA_00001    Bin3_16S        1       1533    +       1533    832450
PROKKA_00002    Bin2_16S        1       1533    +       1533    234918
PROKKA_00003    Bin1_16S        1       1533    +       1533    215641

My question is: how do I properly select a reasonable mapping quality score?

Best and TIA,

Stefano

featureCounts quality score rna-seq • 558 views
ADD COMMENT
1
Entering edit mode

Mapping Q scores are not implemented in the same way by different aligners. Take a look at this blog post for more. If something multi-maps (Q = 0) is probably the best take away.

ADD REPLY
0
Entering edit mode

Thanks @genomax. I think I will go with Q = 0, also because I made trimming and bbmap'd with minid=1, so reads in the SAM file should have already a good quality.

Read the blog and makes me wonder, why are there so few instances of standardisation in bioinformatics? :(

ADD REPLY

Login before adding your answer.

Traffic: 1698 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6