~/work$ rm -R guppy_results

~/work$ rm -R qc_results

~/work$ rm bigfile.fastQ
~/work$ rm aln.sam

~/work$ rm samtools_stats.txt

~/work$ rm -R salmon_qnt.out


ВКЛЮЧИТЬ P3.2XLARGE
~/work$ guppy_basecaller -i fast5 -s guppy_results --qscore_filtering --flowcell FLO-MIN107 --kit SQK-RNA002 --device auto

 SWITCH TO P2.XLARGE

~/work$ MinIONQC.R -i guppy_results/sequencing_summary.txt -o qc_results

~/work$ cat guppy_results/pass/*.fastq > bigfile.fastQ

~/work$ minimap2 -ax map-ont -N 100 ref/gencode.v32.transcripts.fa bigfile.fastQ > aln.sam

~/work$ samtools stats aln.sam > samtools_stats.txt

~/work$ salmon quant -t ref/gencode.v32.transcripts.fa -l U -a aln.sam -o salmon_qnt.out

~/work$ grep "protein_coding" salmon_qnt.out/quant.sf > quant_protcoding.sf

zip -r qc_results.zip qc_results