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toFASTA.sh
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toFASTA.sh
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#!/bin/bash
echo "Creating fasta..."
bedtools getfasta -s -fi $HOME/Desktop/LncRNA_v2/Mouse/mm10_genome/Mus_musculus.GRCm38.dna.primary_assembly.fa -bed $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/rRegs_complete.bed -split -name -fo $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_grouped.fasta
split -l 2664 $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_grouped.fasta $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_grouped
mv $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_groupedaa $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_grouped_aa.fasta
mv $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_groupedab $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_grouped_ab.fasta
mv $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_groupedac $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_grouped_ac.fasta
mv $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_groupedad $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_grouped_ad.fasta
mv $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_groupedae $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_grouped_ae.fasta
mv $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_groupedaf $HOME/Desktop/LncRNA_v2/Mouse/myRegs_cov/lncs_grouped_af.fasta