search

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
98 stars 18 forks source link

Is there a way to update all transcript to complete gene models? #428

Closed xiekunwhy closed 2 years ago

xiekunwhy commented 2 years ago

Hi,

I found that there are many incomplete gene models in mikado output gff file, is there a way to update these models to complete gene models?

Best, Kun

sanyalab commented 2 years ago

Hi Kun,

Try TAMA tools. Plus how are you ascertaining the incompleteness of gene models? Using alignment to reference? This works for very very closely related organisms.

My 2 cents... extract transcripts using gff+genomefasta, gather Iso-Seq genome alignment data (Pacbio/Nanopore), merge using TAMA. Then compare and see what you get.

-Abhijit

swarbred commented 2 years ago

@xiekunwhy

Mikado does not assemble or combine transcripts so this will reflect how fragmented the transcript assemblies were that were provided as input. Without more details I cant really offer much help.