Question: Count non-coding genes using featureCounts
1
gravatar for Yizhao
19 months ago by
Yizhao10
China
Yizhao10 wrote:

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.

sequencing rna-seq alignment • 685 views
ADD COMMENTlink modified 19 months ago by Devon Ryan92k • written 19 months ago by Yizhao10

I've googled this problem very carefully, but I still have no idea about the reason. Thank in advance.

ADD REPLYlink written 19 months ago by Yizhao10
1
gravatar for Devon Ryan
19 months ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

If you want to include non-coding genes then you can't count using CDS as the feature type (they lack that by definition). Remove the -g option so you're using the default exon value.

ADD COMMENTlink written 19 months ago by Devon Ryan92k
1

FYI you should never count reads on CDS, always count on exons for RNA-Seq

ADD REPLYlink written 19 months ago by Nicolas Rosewick8.4k

Thanks for your attention. I 've also tried by submitting "-t exon -g gene_id", which attributes exons to gene-leve meta-feature. Ant the non-coding gene features were not included in the resulting count file either.

ADD REPLYlink written 19 months ago by Yizhao10

Please post a few lines from your GTF including at least one entry for a non-coding gene.

ADD REPLYlink written 19 months ago by Devon Ryan92k

Sorry for the bothering.

ADD REPLYlink written 19 months ago by Yizhao10

Great, thanks very much. I've checked the exon-based counting resulting file. And it includes all I want.

ADD REPLYlink written 19 months ago by Yizhao10
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