scripts/align_bambu_spikein_samples.sh
bambu_spikein_samples=("SGNex_Hct116_directRNA_replicate3_run1" "SGNex_Hct116_directcDNA_replicate3_run2" "SGNex_Hct116_directcDNA_replicate4_run1" "SGNex_Hct116_directcDNA_replicate5_run1" "SGNex_Hct116_cDNA_replicate3_run3" "SGNex_Hct116_cDNA_replicate4_run2" "SGNex_K562_directRNA_replicate4_run1" "SGNex_K562_directRNA_replicate5_run1" "SGNex_K562_directcDNA_replicate4_run2" "SGNex_MCF7_cDNAStranded_replicate3_run2" "SGNex_MCF7_directcDNA_replicate3_run3" "SGNex_MCF7_directRNA_replicate4_run1" "SGNex_MCF7_directcDNA_replicate4_run2" "SGNex_H9_directRNA_replicate2_run1" "SGNex_H9_directRNA_replicate3_run1" "SGNex_H9_directRNA_replicate4_run1" "SGNex_HEYA8_directRNA_replicate1_run1" "SGNex_HEYA8_directRNA_replicate2_run1" "SGNex_H9_directRNA_replicate2_run2" "SGNex_H9_directRNA_replicate3_run2" "SGNex_H9_directRNA_replicate4_run2" "SGNex_HEYA8_directRNA_replicate1_run2" "SGNex_HEYA8_directRNA_replicate2_run2" "SGNex_HEYA8_directRNA_replicate3_run1" "SGNex_HEYA8_directcDNA_replicate1_run3" "SGNex_HEYA8_directcDNA_replicate2_run3" "SGNex_HEYA8_directcDNA_replicate3_run2" "SGNex_H9_directcDNA_replicate2_run3" "SGNex_H9_directcDNA_replicate3_run3" "SGNex_H9_directcDNA_replicate4_run3" "SGNex_HEYA8_cDNA_replicate1_run4" "SGNex_HEYA8_cDNA_replicate2_run4" "SGNex_HEYA8_cDNA_replicate3_run3" "SGNex_H9_cDNA_replicate2_run4" "SGNex_H9_cDNA_replicate3_run4" "SGNex_H9_cDNA_replicate4_run4")

parallel --progress -j 8 'minimap2 -t 8 -ax map-ont -N 100 ../../data/bambu_paper/refs/hg38_sequins_SIRV_ERCCs_longSIRVs_cdna.fa ../../data/bambu_paper/samples/{}.fastq.gz | samtools view -@2 -bS > ../../data/bambu_paper/aln/{}.bam' ::: ${bambu_spikein_samples[@]}
