Command usage .

[dvirdi01]

I have bunch of Oxford long-read fastq files that I need to convert to sorted bam files and later assembly using stringtie. I ran the following command for conversion from fastq files to bam using snakemake:

    minimap2 -t {threads} -a -x map-ont {input.genome} {input.fastq}  | \
    samtools sort -o {output} -@ {threads} - \

Since I did not use the ax-splice option, I wantes to confirm that the files it output were raw long-read sorted files and not alternatively alignment files? It also said to use presets before any other option. I had the threads parameter first so did it produce the wrong output files?

Also, if I want to do a aplice analysis on my files using stringtie, I would be suing this command to convert my fastq files to bam files right?

minimap2 -a -x splice map-ont {input.genome}  {input.fastq} -t {threads}  | \
samtools sort -o {output} -@ {threads} - \