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?