Question: featureCounts output - assignment percentage
gravatar for oma219
2.8 years ago by
oma21930 wrote:


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
rna-seq sequence • 1.1k views
ADD COMMENTlink modified 7 months ago by h.mon29k • written 2.8 years ago by oma21930
gravatar for Devon Ryan
2.8 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

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.

ADD COMMENTlink written 2.8 years ago by Devon Ryan93k
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