Hi,

I would like to use Rsubreads to coutn feature on exon (summarizing at the gene ID level), however featureCounts does not accept my gtf:

...
> || Load annotation file ~/genomes/mus_musculus/mm10/annotation/ensembl_mu ... ||
> Failed to open the annotation file ~/genomes/mus_musculus/mm10/annotation/ensembl_mus_musculus.GRCm38.75.gtf, > or its format is incorrect, or it contains no 'exon' features.
> Error in file(file, "rt") : cannot open the connection
> In addition: Warning message:
> In file(file, "rt") :
>   cannot open file './.Rsubread_featureCounts_pid8772': No such file or directory

What surprise me is that when I run it in bash using featureCounts, same annotation file, I have no problem and got my resut.

Am I doing somehting wrong?

Samuel

Providing the full path to your GTF file should resolve this problem.

Wei

I am not sure, but this error message could also mean that you have no write permission in your current directory where you started R (what I mean is the working directory).

Alternatively, what about providing the full path instead of the ~/?

cheers, jo
 

Thanks Wei and Johanness, full path of gtf was the thing! Should have thought about it...

(sorry for not answering before)