Problems with custom GTF

[Christian Hodar]

Hi,

Im planning use miRNA analysis using custom gtf file from D. melanogaster flybase database, but once the program run, I have this error:

"ERROR Please check that the parameter database inside section [ReadCount] is correct."

My readcount options in my ini file are: [ReadCount] #GFF file used to calculate the number of reads in featureCounts analysis database=/mnt/Raid_Dell/Dmel.genome/gff.flybase/dmel-all-r6.21.gtf ;GFF attribute to be used as feature ID (default: gene_id) for featureCounts analysis seqid=gene_id ;Feature type (3rd column in GFF file) to be used, all features of other type are ignored (default:exon) for featureCounts analysis featuretype=exon

Thanks for the help. Christian.

[Eduardo Andres Leon]

Hi, this error appears because the file does not exists or it can be read.

Have you check if the file: /mnt/Raid_Dell/Dmel.genome/gff.flybase/dmel-all-r6.21.gtf exists and can be accessed?

E

[Christian Hodar]

Yes, is in the folder.

[chodar@Dell-T7500:~]>ls -l /mnt/Raid_Dell/Dmel.genome/gff.flybase/dmel-all-r6.21.gtf

-rw-rw-r-- 1 chodar chodar 77509693 jun 11 10:13 /mnt/Raid_Dell/Dmel.genome/gff.flybase/dmel-all-r6.21.gtf

[Christian Hodar]

Solved. I noticed that gtf files from Ensembl are space-delimited and my file is tab-delimited. Once I move the delimiter, Alignmer parameters run ok.