Entering edit mode
Dear Community,
I'd like to clarify unexpected behaviour of featureCounts when counting on ONT cDNA bam files, generated with minimap2 with the splice alignment preset. FeatureCounts version: 2.1.1. When running
featureCounts -L -C -Q 10 --primary -M -O --fraction -t transcript
aired-end : no ||
|| Count read pairs : no ||
|| Annotation : genes.filtered.gtf (GTF) ||
|| Dir for temp files : /scratch/local/snakepipes.khA6aeMgrY ||
|| ||
|| Threads : 8 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted (fractional) ||
|| Multiple alignments : primary alignment only ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| Long read mode : yes ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Load annotation file genes.filtered.gtf ... ||
|| Features : 267506 ||
|| Meta-features : 67928 ||
|| Chromosomes/contigs : 439 ||
|| ||
|| Process BAM file sorted.bam... ||
|| Single-end reads are included. ||
|| Total alignments : 9121703 ||
|| Successfully assigned alignments : 3639166 (39.9%) ||
|| Running time : 1.37 minutes ||
i.e. ~ 40% of the fragments are counted. In the summary file, I notice 4481575 fragments (~ 49%) are Unassigned:Mapping Quality.
Samtools stats run on the same bam file on the genic regions tells me that <12% of alignments have MAPQ<10.
What could be the reason for the discrepancy between low MAPQ fraction calculated by samtools stats and by featureCounts ?
Best wishes,
Katarzyna