Prolems about long mRNA reads mapping

[lwlive]

I have read the protocol in webpage of xpore (https://xpore.readthedocs.io/en/latest/preparation.html). It recomands us to mapping the long mRNA reads with the following commands "minimap2 -ax map-ont -uf -t 3 --secondary=no <MMI> <PATH/TO/FASTQ.GZ> > <PATH/TO/SAM> 2>> <PATH/TO/SAM_LOG>". I have read the description of the minimap2. It described like following: -x STR preset (always applied before other options; see minimap2.1 for details) [] - map-pb/map-ont: PacBio/Nanopore vs reference mapping - ava-pb/ava-ont: PacBio/Nanopore read overlap - asm5/asm10/asm20: asm-to-ref mapping, for ~0.1/1/5% sequence divergence - splice: long-read spliced alignment - sr: genomic short-read mapping I thought it is better to use "splice" for option "-x" in mRNA mapping. How do you thinks? Could you give me some suggestion?

[jonathangoeke]

Hi @lwlive thanks for the question, can you post this to the discussions? I will reply there

[jonathangoeke]

answered in #69