A bit confused by the new way of performing annotations for AR_comp

[tzhughes]

The way it used to work was just to use the gene definitions ie from what I could tell from my testing, your code was ignoring any exonic records in the GTF file I supplied on the command line.

Now you have created both a gene and an exonic refgene file as part of the distro:

• so is it now possible to pick between working on the gene level or at the exonic level by specifying one or the other file? Or is it always exonic (+ splice sites)?
• will genmod work with the Ensembl GTF files (which contain both gene and exon records) or do these need to be split into separate files?

[moonso]

so is it now possible to pick between working on the gene level or at the exonic level by specifying one or the other file? Or is it always exonic (+ splice sites)?

Right now it only look for compounds among the exonic/splice variants and this will be the default behaviour. I will include a "whole gene" flag, hopefuly today.

will genmod work with the Ensembl GTF files (which contain both gene and exon records) or do these need to be split into separate files?

It handles GTF files with both genes and exons and does the separation in the "Parsing Annotation" step.

Just a remark: If wou plan to use the same annotation over and over in your analysies you only have to provide the -an "your annotation" once. GENMOD will then build db-like files in the annotation folder and use them by default next time the analysis is done without the -an flag.

[tzhughes]

"whole gene" flag

:thumbsup:

And specifying that the default is exonic and whether this applies to all models or only AR_comp