Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?

[martina]

HI,

I'm using featureCounts 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

[Yang LIAO]

Hi Martina,

FeatureCounts doesn't use the read sequences (SEQ) and quality strings (QUAL) in the input SAM or BAM files, unless if you want to have the per-alignment gene-assignment results written into SAM or BAM files (using options "-R SAM" or "-R BAM"). In either case, the absence of SEQ and QUAL won't affect the read counting results.

Cheers,

Yang