| Verzija | Modul |
|---|---|
| 1.3.1 | bioinfo/RSEM/1.3.1 |
| 1.3.3 | bioinfo/RSEM/1.3.3 |
Korištenje
Podaci su preuzeti sa:
| Code Block | ||
|---|---|---|
| ||
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 * |
Ovisno koji nam tool još treba ubacimo u module load. U ovom slučaju nam treba bowtie.
| Code Block | ||
|---|---|---|
| ||
#!/bin/bash #$ -N RSEM-example #$ -cwd #$ -pe *mpisingle 104 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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