diff --git a/seance4/tutorial/scripts_ngs.md b/seance4/tutorial/scripts_ngs.md index 657d46d..9ea7c8b 100644 --- a/seance4/tutorial/scripts_ngs.md +++ b/seance4/tutorial/scripts_ngs.md @@ -48,7 +48,7 @@ $ ls /shared/projects/dubii2020/data/study_cases/Escherichia_coli/bacterial-reg > > output_dir="fastqc-results-v1" > > mkdir -p ${output_dir} > > -> > data=(*.fastq) +> > data=(/shared/projects/dubii2020/data/study_cases/Escherichia_coli/bacterial-regulons_myers_2013/RNA-seq/fastq/*.fastq) > > for fastqc_file in ${data[@]} > > do > > srun fastqc --quiet ${fastqc_file} -o ${output_dir} @@ -68,7 +68,7 @@ $ ls /shared/projects/dubii2020/data/study_cases/Escherichia_coli/bacterial-reg > > output_dir="fastqc-results-v2" > > mkdir -p ${output_dir} > > -> > data=(*.fastq) +> > data=(/shared/projects/dubii2020/data/study_cases/Escherichia_coli/bacterial-regulons_myers_2013/RNA-seq/fastq/*.fastq) > > srun fastqc -t 6 --quiet ${data[@]} -o ${output_dir} & > > wait > > @@ -87,16 +87,16 @@ $ ls /shared/projects/dubii2020/data/study_cases/Escherichia_coli/bacterial-reg > > output_dir="fastqc-results-v3" > > mkdir -p ${output_dir} > > -> > FASTQ_FILES=(*.fastq) +> > FASTQ_FILES=(/shared/projects/dubii2020/data/study_cases/Escherichia_coli/bacterial-regulons_myers_2013/RNA-seq/fastq/*.fastq) > > srun fastqc --quiet ${FASTQ_FILES[$SLURM_ARRAY_TASK_ID]} -o ${output_dir} > >``` {:.answer} > > Pour lancer ces scripts on utilise la commande suivante : > > ```bash -> > $ sbatch ./fastqc_v1.sh /shared/projects/dubii2020/data/study_cases/Escherichia_coli/bacterial-regulons_myers_2013/RNA-seq/fastq/ -> > $ sbatch ./fastqc_v2.sh /shared/projects/dubii2020/data/study_cases/Escherichia_coli/bacterial-regulons_myers_2013/RNA-seq/fastq/ -> > $ sbatch ./fastqc_v3.sh /shared/projects/dubii2020/data/study_cases/Escherichia_coli/bacterial-regulons_myers_2013/RNA-seq/fastq/ +> > $ sbatch ./fastqc_v1.sh +> > $ sbatch ./fastqc_v2.sh +> > $ sbatch ./fastqc_v3.sh > > > > ``` {:.answer}