UMI Tag Header

This shell script tags FASTQ headers of paired reads with unique molecular identifiers (UMIs) without changing the read sequences or Phred quality scores (trimming required in a separate step) and is intended for use with paired-end FASTQ files created using the Lexogen CORALL Total RNA-Seq V2 library prep kit.

See also: https://github.com/Lexogen-Tools/corall_analysis

Usage

This script is designed to be used in a Linux environment. To run the script, issue the following command:

bash umi_tag_header.sh -a <read1.fastq.gz> -b <read2.fastq.gz>

Alternatively, you can make the script executable and run it directly:

chmod +x umi_tag_header.sh ./umi_tag_header.sh -a <read1.fastq.gz> -b <read2.fastq.gz>

The -a and -b options are used to specify the input files. The script will generate two output files with the suffix _processed.fastq.gz.

Testing

This shell script has been tested and confirmed to work on CentOS 7 and Ubuntu. To test the script, download the subA.fq.gz and subB.fq.gz files in the test_data folder to a suitable directory and execute:

bash umi_tag_header.sh - a subA.fq.gz -b subB.fq.gz

Dependencies

This script requires zcat, awk, and gzip to be installed and available in your PATH.

Reference

Pending.