How do I decide the mapping quality score in featureCounts?

Question

[dark.lord]

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

[GenoMax]

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.

[dark.lord]

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? :(