gravatar for dark.lord

2 hours ago by

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



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