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wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.31_GRCh38.p5/GCF_000001405.31_GRCh38.p5_genomic.fna.gz wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.31_GRCh38.p5/GCF_000001405.31_GRCh38.p5_genomic.gff.gz gzip -d * |
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U ovaj module ubačeni su i drugi moduli:
- bowtie
- STAR
- HISAT2
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#!/bin/bash
#$ -N RSEM-example
#$ -cwd
#$ -pe *mpisingle 4
module load bioinfo/RSEM/1.3.3
module load bioinfo/bowtie/1.3.1
rsem-prepare-reference --gff3 GCF_000001405.31_GRCh38.p5_genomic.gff --gff3-RNA-patterns mRNA,rRNA --trusted-sources BestRefSeq,Curated\ Genomic --bowtie GCF_000001405.31_GRCh38.p5_genomic.primary_assembly.fna ref/human_refseq -p $NSLOTS |
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