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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
300 stars 82 forks source link

Stringtie in fun-predict #982

Open DiegoSafian opened 7 months ago

DiegoSafian commented 7 months ago

Hi, I do not have an issue. Instead, I have a question about how funannotate predict uses --stringtie gtf in gene prediction.

I have RNA-seq data from several tissues and I am looking for the best option to add them to funannotate predict. I thought I could use STAR to align each data set separately, then convert the BAMs into transcripts using StringTie to finally merge all the gtf from Stringtie (one gtf per tissue) with TACO (https://tacorna.github.io/). The idea would be to add the TACO gtf in the funannotate predict --stringtie taco.gtf. Does this sound right??

My best, Diego

hyphaltip commented 7 months ago

Or you can concate them all into R1 and R2 files and give to funannotate train (which might be slow for a giant dataset)? But your approach should work too in that you can provide pre-computed exon info in that manner.