I have a couple of questions regarding parameter choices for featureCounts. I have stranded 150 bp paired-end reads.
I have currently chosen the following settings. As far as I understand, this will count fragments rather than reads, will ignore chimeric fragments, and will count multimapping reads fractionally (primary alignments only; I have set my STAR mapping to output all alignments with the best score as primary alignments).
featureCounts -p -B −−countReadPairs -C -F GTF --verbose -M --fraction --primary -A chromosome_name_alias.txt -T 4 -s 2 -g gene_id -a Homo_sapiens.GRCh38.103.gtf -o counts.txt input.bam
I am interested in whether you would recommend to adjust the
nonOverlap parameters. By default,
minOverlap is 1 - is this sufficient to confidently assign a read to a feature?
I don't fully understand the
maxMOp parameter. Is anyone able to provide a simple explanation?
Many thanks for the suggestions.