Question

gff error in featureCounts

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esu2001 • 0

@esu2001-12022

Last seen 7.4 years ago

Hi,

I am trying to count the number of genes with featureCounts (subread1.5.1-source). I use -a my annotation.gff but it gives me error

WARNING no features were loaded in format GTF.

annotation format can be specified using '-F'. ||

Failed to open the annotation file my annotation.gff, or its format is incorrect, or it contains no 'exon' features.

It is a retroviral genome. So what can I do?

Thanks,

Esma

differential gene expression • 3.2k views

ADD COMMENT • link 7.4 years ago esu2001 • 0

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The file exists. I downloaded it from NCBI website and used it for STAR alignment. It has pretty much everything that a gff file has to have. nothing seems wrong. STAR accepted this file. So i don't know why featureCounts does not!

I thought maybe a different command is needed for gff like we use something different in STAR?

ADD REPLY • link 7.4 years ago esu2001 • 0

score 0 · Answer 1 · 2016-12-15

Well, the error message seems pretty informative.

Have you actually created a GFF file? Is the file name correct? Does the fact actually exist? If the file exists, what does it contain?

The annotation file that you use for read counting obviously has to be different from the genome definition file that you use for alignment. For alignment, you need to define the genome. For read counting, you need to define genes and exons.

Have you read the featureCounts documentation?