I have a question regarding minimap2. For my biological problem, I am doing differential expression analysis and differential transcript usage for six (3 vs 3) samples, which have been sequenced using a cDNA protocol with MinIOn. To start I built a genome-guided transcriptome using minimap2 + stringtie. During the alignment step this is the comand I have used:
minimap2 -t 8 -ax splice cro_v2_asm.mmi 01_filtering/after_trim/all_reads_nano.fastq > 02_annotation/all_reads.sam samtools view -q 40 -b -F 2304 02_annotation/all_reads.sam | samtools sort -@ 8 -o all_reads_filtered.bam samtools index all_reads_filtered.bam
Recently I saw a post suggesting that aligning Nanopore reads should be performed using the -ax map-ont option. However, since reading the manual, I assumed this option was reserved for genomic reads, which I assumed was reads obtained from genome sequencing.
From the minimap2 manual:
./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam # Oxford Nanopore genomic reads ./minimap2 -ax splice ref.fa rna-reads.fa > aln.sam # spliced long reads (strand unknown)
The question arose as to when I was messing with GitHub pipelines for DEG, one of the pipelines used the minimap2 map-ont option to map long reads to a transcriptome, hence my confusion regarding the manual.
What is usually the best present when mapping ONT RNA-seq reads to a genome?