How does --primary work with -M and --fractional options featureCounts?
Hi,
I am trying to understand how the -M, --primary and --fractional work together in featureCounts. From my understanding, -M is ignored if you add the --primary flag. However, what setting should I use if I want to count primary alignments fractionally? Some reads have multiple primary alignments since I have set --outSAMprimaryFlag to AllBestScore in STAR, so all alignments with the best score will be output as primary alignments.
Best wishes,
Lucy
1 answer
If you want full control over the alignments then I would recommend filtering the BAM file prior to counting.
In your case make a new BAM file that contains only the primary alignments.
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Istvan Albert
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