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CompSynBioLab-KoreaUniv / FunGAP

FunGAP: fungal Genome Annotation Pipeline
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about the sofyware #71

Closed ld9866 closed 2 years ago

ld9866 commented 3 years ago

Hello, I see the software you published. Now I want to use it. The species we assembled is a mammal with a genome size of 2.5G. Can I directly use your software to complete the four parts of repeat region, ab initio prediction, homology prediction and annotation merging?

mbnmbn00 commented 3 years ago

Hello,

The gene predictors used in the FunGAP are eukaryotic gene predictors, so it is possible to use the FunGAP on your mammal genome.

Four options you may consider:

  1. --no_braker_fungus No --fungus flag in BRAKER for non-fungus genomes
  2. --no_jaccard_clip No --jaccard_clip flag in Trinity for non-fungus genomes
  3. --no_genemark_fungus No --fungus flag in GeneMark for non-fungus genomes
  4. --max_intron Max intron length (Default: 2000 bp)

I wonder if you sequenced RNA for annotation because FunGAP only works with RNA data.