This is a bash script to standarised different types of fastq files names.
First, give the correct permission to the script.
$ chmod 751 path/rename.sh
Run the script in the directiony where the files are placed.
$ ls
name_1_001.fq.gz name_2_001.fq.gz
name_1.fq.gz name_2.fq.gz
name_1_001.fastq.gz name_2_001.fastq.gz
name_1.fastq.gz name_2.fastq.gz
$ ./Rename_PE.sh
Convert:
name_1_001.fq.gz -> name_R1.fastq.gz
name_2_001.fq.gz -> name_R2.fastq.gz
name_1_001.fastq.gz -> name_R1.fastq.gz
name_2_001.fastq.gz -> name_R2.fastq.gz
name_1.fq.gz -> name_R1.fastq.gz
name_2.fq.gz -> name_R2.fastq.gz
name_1.fastq.gz -> name_R1.fastq.gz
name_2.fastq.gz -> name_R2.fastq.gz
Run the script in the directiony where the files are placed.
$ ls
name.fq.gz
name.fastq.gz
name_001.fq.gz
name_001.fastq.gz
name_1.fq.gz
name_1.fastq.gz
$ ./Rename_SE.sh
Convert:
name.fq.gz -> name_R1.fasta.gz
name.fastq.gz. -> name_R1.fasta.gz
name_001.fq.gz. -> name_R1.fasta.gz
name_001.fastq.gz -> name_R1.fasta.gz
name_1.fq.gz. -> name_R1.fasta.gz
name_1.fastq.gz. -> name_R1.fasta.gz
Usage: Call the script with the input folder, output folder, and number of jobs. If the number of jobs is not specified, the default is 4.
Notes: Do not include a trailing slash (/) in the input or output folder paths. Ensure GNU Parallel is installed (e.g., with conda: conda install -c conda-forge parallel).
Example:
$./Concatenate_fastq.sh input_folder output_folder 6