Gff3 error message

[sebel76]

Dear Micheal,

I got an error message when I use your script using the -g reference mode. See the following message:

*** FATAL: The loci defined in your GFF3 file overlap with each other. This is not allowed. Offending loci: ***

Four your information, I work on barley data (including sRNA-seq, mRNA-seq and PARE-seq) using the ensembl38 genome and annotation references (ftp://ftp.ensemblgenomes.org/pub/plants/release-38/).

Any recommendation to solve the problem?

Thanks, Sébastien

[MikeAxtell]

Hi Sebastien, thanks for your message. As the message states, this program does not allow overlapping intervals .. this would cause double- or more counting of the same genomic coordinates.

I would suggest just converting the whole alignment, as opposed to only certain intervals.

I'd also like to point out that I myself don't use this code anymore. It's rather slow compared to bamCoverage , which is from the deeptools suite ( http://deeptools.readthedocs.io/en/develop/)

Best, Mike

On Tue, Jun 12, 2018 at 1:41 PM sebel76 [email protected] wrote:

Dear Micheal,

I got an error message when I use your script using the -g reference mode. See the following message:

*** FATAL: The loci defined in your GFF3 file overlap with each other. This is not allowed. Offending loci: ***

Four your information, I work on barley data (including sRNA-seq, mRNA-seq and PARE-seq) using the ensembl38 genome and annotation references ( ftp://ftp.ensemblgenomes.org/pub/plants/release-38/).

Any recommendation to solve the problem?

Thanks, Sébastien

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[sebel76]

Thanks Micheal for your quick reply! According to your suggestion, I will use bamCoverage to acquire a higher speed for this task!

Best regards, Sébastien