Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
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@8c5b5ddd
Last seen 9 months ago

HI, I'm using featureCounts (a sw provided by the Subread package) to count reads taken from a BAM file without the SEQ - QVAL fields.

The read summation routine gives the expected results with the following parameters:

featureCounts -M -a data/basicAnnotation.gtf -o result/basic_M.FC  data/basic.bam.


I’m wondering if the absence of the SEQ/QVAL fields in the input file could be an issue when using any of the other optional arguments provided by the command line function of featureCounts.