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Now let’s prepare a samplesheet.csv file that specifies the name of your samples and the location of the raw FASTQ files
| Code Block |
|---|
sample,fastq_1
SRR24302008,/path/to/raw/FASTQ/files/SRR24302008.fastq.gz
SRR24302009,/path/to/raw/FASTQ/files/SRR24302009.fastq.gz
SRR24302010,/path/to/raw/FASTQ/files/SRR24302010.fastq.gz
SRR24302011,/path/to/raw/FASTQ/files/SRR24302011.fastq.gz
SRR24302012,/path/to/raw/FASTQ/files/SRR24302012.fastq.gz
SRR24302013,/path/to/raw/FASTQ/files/SRR24302013.fastq.gz
SRR24302014,/path/to/raw/FASTQ/files/SRR24302014.fastq.gz
SRR24302015,/path/to/raw/FASTQ/files/SRR24302015.fastq.gz
SRR24302016,/path/to/raw/FASTQ/files/SRR24302016.fastq.gz
SRR24302017,/path/to/raw/FASTQ/files/SRR24302017.fastq.gz
SRR24302018,/path/to/raw/FASTQ/files/SRR24302018.fastq.gz
SRR24302019,/path/to/raw/FASTQ/files/SRR24302019.fastq.gz
SRR24302020,/path/to/raw/FASTQ/files/SRR24302020.fastq.gz
SRR24302021,/path/to/raw/FASTQ/files/SRR24302021.fastq.gz
SRR24302022,/path/to/raw/FASTQ/files/SRR24302022.fastq.gz
SRR24302023,/path/to/raw/FASTQ/files/SRR24302023.fastq.gz
SRR24302024,/path/to/raw/FASTQ/files/SRR24302024.fastq.gz
SRR24302025,/path/to/raw/FASTQ/files/SRR24302025.fastq.gz
SRR24302026,/path/to/raw/FASTQ/files/SRR24302026.fastq.gz
SRR24302027,/path/to/raw/FASTQ/files/SRR24302027.fastq.gz |
To generate the above file, let’s use the following PBS Pro script (i.e., called “launch_create_smRNAseq_samplesheet.pbs”)
| Code Block |
|---|
#!/bin/bash -l
#PBS -N nfsmrnaseq
#PBS -l select=1:ncpus=2:mem=4gb
#PBS -l walltime=12:00:00
#work on current directory (folder)
cd $PBS_O_WORKDIR
#User defined variables
##########################################################
DIR='/path/to/raw/FASTQ/files'
INDEX='samplesheet.csv'
##########################################################
#load python module
module load python/3.10.8-gcccore-12.2.0
#fetch the script to create the sample metadata table
wget -L https://raw.githubusercontent.com/nf-core/rnaseq/master/bin/fastq_dir_to_samplesheet.py
chmod +x fastq_dir_to_samplesheet.py
#generate initial sample metadata file
./fastq_dir_to_samplesheet.py $DIR index.csv \
--strandedness auto \
--read1_extension .fastq.gz
#format index file
cat index.csv | awk -F "," '{print $1 "," $2}' > ${INDEX}
#Remove intermediate files:
rm index.csv fastq_dir_to_samplesheet.py |
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