featureCounts output - assignment percentage

Question

[oma219]

Hello,

I was using featureCounts to produce gene counts but its only able to assign 26.3 of the reads to a gene. Is that a common percentage and are there any options I may be missing that could increase that percentage? Thanks!

featureCounts -f -t exon  -g Name -a /home/ubuntu/data/rnaseq/nematostella/venus/genome/Nemostella_New_Annotation.gff3 -o DICDvenus2_counts_featureCounts.txt /home/ubuntu/data/rnaseq/nematostella/venus/alignment/DICDvenus2_STARAligned.out.sam

Answer 1

[Devon Ryan]

While that would be low for some organisms (e.g., mouse), it may be within the norm for yours. Have a look at your BAM files in IGV. My guess is that the annotation for your organism isn't the highest quality, so there are many unannotated transcripts and genes. There's nothing featureCounts can do about that.