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The objective

Caculate the mean read length of Paired end fastq files

Getting started

To get started on using the scripts, the overarching directory PE_read, which contains all the needed files, scripts and directories. User need to change the path(work_dir) in Setting.txt. And run the command below on server or in terminal.

python3.7 readlength.py Setting.txt

Lay-out of directories and files.

users need to store data in the layout shown as below. (See test data)

  • readlength.py

  • Setting.txt

  • testdata

    • Paired_end_fastq_files1

      • Read_1_fastq

      • Read_2_fastq

    • Paired_end_fastq_files2

      • Read_1_fastq

      • Read_2_fastq