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a-slide / pycoMeth

DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets
GNU General Public License v3.0
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Is it possible to use `Comp_Report` without a gff3 file? #38

Closed jolespin closed 2 years ago

jolespin commented 4 years ago

I'm working on a project where we are not considering annotations. There are also no gene models for our organism so we have no gff3 available. Is it possible to still use Comp_Report without a gff3 file to get a report of differential methylation events by intervals?

https://adrienleger.com/pycoMeth/Comp_Report/CLI_usage/

a-slide commented 4 years ago

Unfortunately no, at the moment it is expecting a a GFF3 file and in my opinion it is 90% of the interest of the report. Now, you are right it could be an interesting option to still get the 10% left for non-annotated organisms. I will keep that open as a feature request but I am not going to be able to implement that in the next 3 or 4 weeks. I will be happy to take a Pull Request if you want to try implementing it. A quick and dirty alternative (although I am not 100% sure it will work) would be to use a decoy GFF file from yeast for example or maybe an empty file.