VerzijaModul
4.1bioinfo/cutadapt/4.1

Korištenje:

Datoteke korištene u primjerima: https://zenodo.org/record/3736457


Primjer 1:

Trimmer
#!/bin/bash
#$ -N cutadapt-simple
#$ -pe a16-mpisingle 2
#$ -cwd

module load bioinfo/cutadapt/4.1

cutadapt -u -100 -o trimmed.fastq sample_1.fastq.gz

Primjer 2:

Trimmer sa više jezgri
#!/bin/bash
#$ -N cutadapt-simple
#$ -pe a16-mpisingle 10
#$ -cwd

module load bioinfo/cutadapt/4.1

cutadapt -j $NSLOTS -u -100 -o trimmed.fastq sample_1.fastq.gz

Instalacija

conda instalacija
conda create -p /apps/virtenv/cutadapt4.1
conda activate /apps/virtenv/cutadapt4.1
conda install -c bioconda cutadapt
cutadapt --version
  • No labels