current dir:	/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/code
mapper command:	/home/shared/mirdeep2/bin/mapper.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11.1-Apul-sRNAseq-miRdeep2-31bp-fastp-merged/collapsed-reads-all-mirdeep2.fasta -c -p /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic-no_spaces -t /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11.1-Apul-sRNAseq-miRdeep2-31bp-fastp-merged/Apul-mirdeep2-mapping.arf -o 40

timestamp:	01_04_2024_t_19_20_52

discarding short reads
fastaparse.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11.1-Apul-sRNAseq-miRdeep2-31bp-fastp-merged/collapsed-reads-all-mirdeep2.fasta -a 18 > dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_9203885952_01_04_2024_t_19_20_52/reads_no_short.fa 2>dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_9203885952_01_04_2024_t_19_20_52/reads_too_short
mapping reads to genome index
bowtie -p 40 -f -n 0 -e 80 -l 18 -a -m 5 --best --strata  /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic-no_spaces  --al dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_9203885952_01_04_2024_t_19_20_52/collapsed-reads-all-mirdeep2.fasta_mapped --un dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_9203885952_01_04_2024_t_19_20_52/collapsed-reads-all-mirdeep2.fasta_not_mapped  dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_9203885952_01_04_2024_t_19_20_52/reads_no_short.fa dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_9203885952_01_04_2024_t_19_20_52/mappings.bwt 2>bowtie.log

convert_bowtie_output.pl dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_9203885952_01_04_2024_t_19_20_52/mappings.bwt > dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_9203885952_01_04_2024_t_19_20_52/mappings.arf
trimming unmapped nts in the 3' ends
parse_mappings.pl dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_9203885952_01_04_2024_t_19_20_52/mappings.arf -j > dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_9203885952_01_04_2024_t_19_20_52/mappings_trim.arf

remove tmp dir
rmtree(dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_9203885952_01_04_2024_t_19_20_52)

############################################################