VerzijaModul
1.8.1bioinfo/detonate/1.8.1

Korištenje

Primjer
#!/bin/bash
#$ -N detonate-test
#$ -cwd
#$ -pe *mpisingle 8

module load bioinfo/detonate/1.8.1

rsem-eval-calculate-score examples/toy_SE.fq examples/toy_assembly_1.fa ./rsem_eval_1 76 --transcript-length-parameters true_transcript_length_distribution/mouse.txt -p $NSLOTS

Dostpne komande:

ref-eval
ref-eval-estimate-true-assembly

rsem-bam2readdepth
rsem-bam2wig
rsem-build-read-index
rsem-calculate-credibility-intervals
rsem-eval-calculate-score
rsem-eval-estimate-transcript-length-distribution
rsem-extract-reference-transcripts
rsem-gen-transcript-plots
rsem-get-unique
rsem-parse-alignments
rsem-plot-model
rsem-plot-transcript-wiggles
rsem-preref
rsem-run-em
rsem-run-gibbs
rsem-sam-validator
rsem-scan-for-paired-end-reads
rsem-simulate-reads
rsem-synthesis-reference-transcripts
rsem-tbam2gbam


Instalacija

  • potreban modul Bowtie
  • potreban modul Samtools
  • Instalacija je izvršena prevodiocem intel/2019
wget https://github.com/deweylab/detonate/archive/refs/tags/1.8.1.tar.gz
module load intel/2019
CC=icc CXX=icpc make
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