scripts/quant_bambu_spikein_samples_nanocount.sh
samples_drna=("SGNex_Hct116_directRNA_replicate3_run1" "SGNex_K562_directRNA_replicate4_run1" "SGNex_K562_directRNA_replicate5_run1" "SGNex_MCF7_directRNA_replicate4_run1")
samples_cdna=("SGNex_Hct116_cDNA_replicate3_run3" "SGNex_Hct116_cDNA_replicate4_run2" "SGNex_Hct116_directcDNA_replicate3_run2" "SGNex_Hct116_directcDNA_replicate4_run1" "SGNex_Hct116_directcDNA_replicate5_run1" "SGNex_K562_directcDNA_replicate4_run2" "SGNex_MCF7_cDNAStranded_replicate3_run2" "SGNex_MCF7_directcDNA_replicate3_run3" "SGNex_MCF7_directcDNA_replicate4_run2")

## using GNU parallel
#parallel --progress -j 16 'NanoCount -t -1 -x -n -i ../../data/bambu_paper/aln/{}.bam -o ../../data/bambu_paper/quants/nanocount/{}.tsv' ::: ${samples_cdna[@]}
#parallel --progress -j 16 'NanoCount -x -i ../../data/bambu_paper/aln/{}.bam -o ../../data/bambu_paper/quants/nanocount/{}.tsv' ::: ${samples_drna[@]}

## using rush (Go program)
RUSH=~/go/bin/rush
# for the cDNA samples, we allow negative strand alignments, and we turn off the 
# 3' filtering criterion.
echo ${samples_cdna[@]} | $RUSH -j 16 --eta -T "r" -D " " "NanoCount -t -1 -x -n -i ../../data/bambu_paper/aln/{}.bam -o ../../data/bambu_paper/quants/nanocount/{}.tsv"
# for the directRNA samples we use the defaults (but include extra info in the output)
echo ${samples_drna[@]} | $RUSH -j 16 --eta -T "r" -D " " "NanoCount -x -i ../../data/bambu_paper/aln/{}.bam -o ../../data/bambu_paper/quants/nanocount/{}.tsv"

