Nanopore Iso-Seq without Illumina

[francicco]

Description of bug

Hi,

I have ~50M reads of Iso-Seq Nanopore data, but I don't have illumina RNAseq. I'd like to assemble the reads and map the transcripts to the genome to perform the genome annotation.

My understanding is that rnaSpades only perform a hybrid approach.
Is that correct or there's anything I'm missing here?

Thanks a lot
F

spades.log

Don't have it

params.txt

Don't know

SPAdes version

3.15

Operating System

CentOS

Python Version

Phython 3

Method of SPAdes installation

binaries

No errors reported in spades.log

• Yes

[andrewprzh]

Dear @francicco

You are right, rnaSPAdes only supports hybrid approach.
Since you have a genome, I would recommend you to use a reference-based tool, for example IsoQuant. It will generate a GTF annotation right from your Nanopore data.

Best
Andrey

[francicco]

Hi @andrewprzh,

That is a great tip! Thanks a lot.
Best
F