featureCounts -L: high unassigned:mapq fraction
0
0
Entering edit mode
sikora • 0
@694bee18
Last seen 9 days ago
Germany

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

Bioconductor • 40 views
ADD COMMENT

Login before adding your answer.

Traffic: 586 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