current dir:	/home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/code
mapper command:	/home/shared/mirdeep2/bin/mapper.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/11-Peve-sRNAseq-miRdeep2/collapsed-reads-all-mirdeep2.fasta -c -p /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/data/Porites_evermanni_v1_genomic-no_spaces -t /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/11-Peve-sRNAseq-miRdeep2/Peve-mirdeep2-mapping.arf -o 46

timestamp:	01_12_2023_t_10_12_00

discarding short reads
fastaparse.pl /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/E-Peve/output/11-Peve-sRNAseq-miRdeep2/collapsed-reads-all-mirdeep2.fasta -a 18 > dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_4738794861_01_12_2023_t_10_12_00/reads_no_short.fa 2>dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_4738794861_01_12_2023_t_10_12_00/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/E-Peve/data/Porites_evermanni_v1_genomic-no_spaces  --al dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_4738794861_01_12_2023_t_10_12_00/collapsed-reads-all-mirdeep2.fasta_mapped --un dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_4738794861_01_12_2023_t_10_12_00/collapsed-reads-all-mirdeep2.fasta_not_mapped  dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_4738794861_01_12_2023_t_10_12_00/reads_no_short.fa dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_4738794861_01_12_2023_t_10_12_00/mappings.bwt 2>bowtie.log

convert_bowtie_output.pl dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_4738794861_01_12_2023_t_10_12_00/mappings.bwt > dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_4738794861_01_12_2023_t_10_12_00/mappings.arf
trimming unmapped nts in the 3' ends
parse_mappings.pl dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_4738794861_01_12_2023_t_10_12_00/mappings.arf -j > dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_4738794861_01_12_2023_t_10_12_00/mappings_trim.arf

remove tmp dir
rmtree(dir_mapper_seq_collapsed-reads-all-mirdeep2.fasta_4738794861_01_12_2023_t_10_12_00)

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