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EI-CoreBioinformatics / mikado

Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.
https://mikado.readthedocs.io/en/stable/
GNU Lesser General Public License v3.0
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[URGENT] Daijin needs to be able to specify the minimum ORF length for TransDecoder #89

Closed lucventurini closed 8 years ago

lucventurini commented 8 years ago

At the moment Daijin executes TransDecoder without asking for the minimum length of the ORF to be found. The default, 100 AA or 300 bps, is too high for Mikado as the tool relies on the coding signal for many purposes. I suspect that many of the issues I have with the simulated data derive from the setting being too high; there are thousands of reconstructable transcripts with an ORF shorter than 100 AA, which we lose as putative fragments.

maplesond commented 8 years ago

Should be fixed in the latest version of the development branch. However, I couldn't fully test this out this morning as SLURM wasn't allowing jobs to run correctly. We will need to test properly later today.

lucventurini commented 8 years ago

Fixed in 1.0.0b3.