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.

Thank you in advance for any help you could provide