FeatureCounts dont read all features

Question

[David]

Dear all,

I think I may have a problem importing GTF file into featureCounts cause it only import 121 features out of 3K+ features. I got my GTF files from genbank assembly (https://www.ncbi.nlm.nih.gov/assembly/GCF_000021625.1) without any modification;

> fc <- featureCounts(bam.files, isGTFAnnotationFile=TRUE, annot.ext="/Users/RNAseq/GCF_009646135.1_ASM964613v1_feature_table.gtf")

Load annotation file GCA_000016245.1_ASM1624v1_genomic.gtf ...             ||
||    Features : 121                                                          ||
||    Meta-features : 121                                                     ||
||    Chromosomes/contigs : 2    

Any idea what the problem is?

Thanks

Answer 1

[Carlo Yague]

By default, featureCounts considers only exons as features.

 -t <string>         Specify feature type in GTF annotation. `exon' by 
                      default. Features used for read counting will be 
                      extracted from annotation using the provided value.

In this annotation, there is only 127 exons... so it considers only those.

 cut -f 3 GCF_000021625.1_ASM2162v1_genomic.gtf | sort | uniq -c
3733 CDS
 127 exon
3854 gene
3727 start_codon
3727 stop_codon

To correct this behaviour, use option -t 'gene" which make more sense with prokaryotes anyway.

[David]

Yes, that makes sense, and it works now... Thank you very much for your help! Cheers

[GenoMax]

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