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conJUSTover / pSONIC

The repository serves as a public and official hosting of the pSONIC program (Conover et al., 2021).
GNU General Public License v3.0
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Prepare files for MCScanX Wiki mistake #1

Closed SJ-Smit closed 3 years ago

SJ-Smit commented 3 years ago

The instructions in the wiki under "2. Prepare files for MCScanX" is incorrect. The gff order for mcscanx should be Sp## GeneID Start_POS End_POS.

conJUSTover commented 3 years ago

Ah, thanks for catching this! I've updated the README to correct this error.

SJ-Smit commented 3 years ago

Thanks. One more tiny thing. The Orthogroups output on my side is by default saved as .tsv eventhough it is actualy a csv file. I manually changed the extension to csv. Kept getting an error when running translate_gff until I changed the extension.

conJUSTover commented 3 years ago

That is a change that OrthoFinder implemented after I wrote that block of code. The format between the .csv and the .tsv didn't change from what I can tell, so your run shouldn't be affected.

I've created a new issue to fix this. In the meantime, when using --translate_gff I believe you can use the -og flag and feed it a file with the .tsv extension, and it should still work fine. It's a more reproducible alternative than manually changing your file extension.