Yes that´s a metagenomics experiment on skin, i´m not interested in human , but bacteria and fungi.
For some reasons fungi are filtered out:
This is the command line:
# Map ONT reads to human genome
minimap2 -t10 -ax map-ont human_p38.3.fa ONT.reads.fq | samtools view --threads 10 -Sb - > mapping.human.bam
# Get nanopore reads unmapped to human genome
samtools view --threads 10 -b -f 4 -F 0x900 mapping.human.bam > human.unmapped.bam
samtools sort...
samtools fastq...
#Get ONT reads mapped to the human genome
samtools view --threads 10 -b -F4 -F0x900 human.mapping.bam > human.mapped.bam
samtools sort...
samtools fastq...
Is that ok ?
