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 <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?
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 <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) []