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-Apul-sRNAseq-miRdeep2/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-Apul-sRNAseq-miRdeep2/Apul-mirdeep2-mapping.arf -o 46

timestamp:	08_11_2023_t_13_53_31

discarding short reads
fastaparse.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/output/11-Apul-sRNAseq-miRdeep2/collapsed-reads-all-mirdeep2.fasta -a 18 > dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_5931181836_08_11_2023_t_13_53_31/reads_no_short.fa 2>dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_5931181836_08_11_2023_t_13_53_31/reads_too_short
mapping reads to genome index
bowtie -p 46 -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_5931181836_08_11_2023_t_13_53_31/collapsed-reads-all-mirdeep2.fasta_mapped --un dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_5931181836_08_11_2023_t_13_53_31/collapsed-reads-all-mirdeep2.fasta_not_mapped  dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_5931181836_08_11_2023_t_13_53_31/reads_no_short.fa dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_5931181836_08_11_2023_t_13_53_31/mappings.bwt 2>bowtie.log

convert_bowtie_output.pl dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_5931181836_08_11_2023_t_13_53_31/mappings.bwt > dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_5931181836_08_11_2023_t_13_53_31/mappings.arf
trimming unmapped nts in the 3' ends
parse_mappings.pl dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_5931181836_08_11_2023_t_13_53_31/mappings.arf -j > dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_5931181836_08_11_2023_t_13_53_31/mappings_trim.arf

remove tmp dir
rmtree(dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_5931181836_08_11_2023_t_13_53_31)

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