Hi all,

I try to count aligned reads from RNA-Seq using featureCounts. I used the comprehensive GTF file as annotation downloaded from Ensembl database, which included both protein_coding and non-coding genes annotation. featureCounts output a count file and a summary file as something like we want.

But I found the count file didn't include non-coding gene features of which the annotation was included in my GTF file.

Anybody else notice this problem?

Parameter list I submitted was:

 featureCounts -F 'GTF' -t 'CDS' -g 'gene_id' -Q 20 -d 20 -C -s 0 -T ${ncore} \
              -a ${gtf_file} -o ${featurecount_dir}/${raw_fq_dir}/counts.cds \
              ${star_align_dir}/${raw_fq_dir}/star.sorted.bam

Thanks in advance.