Use trinity transcripts instead of RNA-seq reads

[Kapeel]

Hi,

I see Lorean uses Trinity to assemble the short RNA-seq reads. I have a data thats already assembled with Trinity, can I just pass the assembled Trinity.fasta to Lorean. What option should I select?

Also, I have the polished Iso-seq hq transcripts instead of raw FASTQ files. Can I use them with -lr option.

Thanks

Kapeel

[lfaino]

Hi,
unfortunately it is not possible. Short reads are used in several ways like Augustus training and it is not possible to exclude Trinity at the moment.
You can use Iso-seq polished. Actually, it is better.

cheers
Luigi