Hi - I'm trying to generate a sashimi plot using data from Oxford Nanopore sequencing of cDNA amplicons. I've aligned my fastq files to the genome using minimap2, converted to bam files and sorted and indexed. IGV appears to recognize linked alignments from each read, but the splice junctions track is empty and the sashimi plot I'm able to generate shows no junctions. I'm guessing this is a problem with how I generated the bam files - if anyone can give me some tips on what might fix the problem I'd appreciate it. Thanks, Brad

My alignment script:

module load minimap2/2.17

minimap2 /home/software/cellranger-atac/reference/GRCh38/fasta/genome.fa Barcode01.fastq > BC01alignment.sam -ax map-ont

module load samtools/1.10

samtools view -bS BC01alignment.sam > BC01alignment.bam

samtools sort BC01alignment.bam > BC01alignmentsorted.bam

samtools rmdup BC01alignmentsorted.bam BC01Final.bam

samtools index -b BC01Final.bam BC01Final.bai

.bam visualized in IGV: https://i.imgur.com/ac6CivE.png

Sashimi plot with no splice junctions: https://i.imgur.com/wXPp8RK.png