minimap2 setting for RNAseq of 150PE

Question

[hans]

Hello I need to map Illumina's 150PE RNAseq reads to a reference genome. I wonder if minimap is suitable for this task or I should use different software. The goal of the mapping is variant calling. If minimap is a good choice, which parameters should I use? Thank you

Answer 1

[ATpoint]

Minimap2 is commonly used for long reads (Nanopore and company...) while for Illumina short reads one typically uses tools such as most commonly Hisat2 or STAR. They obviously need to be splice-aware which these two are (so is minimap2 but as said it is usually used for long reads). Any of the two should be a good choice.

[hans]

I eventually found the the answer in minimap manual: "Minimap2 does not work well with short spliced reads. There are many capable RNA-seq mappers for short reads."