Supported sample filename formats (Regex)

Owned by Gábor Józsa
Last updated: Aug 09, 2023 by Adam Nagyhazy-Horvath
1 min read

Single-end:


    (?P<sample_name>[^_]*)_(?P<lane_num>[0-9]*)\.fastq\.gz
    (?P<sample_name>[^_]*)_(?P<lane_num>[0-9]*)\.fastq
    (?P<sample_name>[^_]*)_L(?P<lane_num>[0-9]*)\.fastq\.gz
    (?P<sample_name>[^_]*)_L(?P<lane_num>[0-9]*)\.fastq
    (?P<sample_name>[^_]*)_(?P<lane_num>[0-9]*)\.fq\.gz
    (?P<sample_name>[^_]*)_(?P<lane_num>[0-9]*)\.fq
    (?P<sample_name>[^_]*)_L(?P<lane_num>[0-9]*)\.fq\.gz
   (?P<sample_name>[^_]*)_L(?P<lane_num>[0-9]*)\.fq

Paired-end:


    (?P<sample_name>[^_]*)_L(?P<lane_num>[0-9]*)_R(?P<pair_num>1|2)\.fastq\.gz
    (?P<sample_name>[^_]*)_L(?P<lane_num>[0-9]*)_R(?P<pair_num>1|2)\.fastq
    (?P<sample_name>[^_]*)_.*_L(?P<lane_num>[0-9]*)_R(?P<pair_num>1|2)_001\.fastq\.gz
    (?P<sample_name>[^_]*)_.*_L(?P<lane_num>[0-9]*)_R(?P<pair_num>1|2)_001\.fastq
    (?P<sample_name>[^_]*)_L(?P<lane_num>[0-9]*)_R(?P<pair_num>1|2)\.fq\.gz
    (?P<sample_name>[^_]*)_L(?P<lane_num>[0-9]*)_R(?P<pair_num>1|2)\.fq
    (?P<sample_name>[^_]*)_.*_L(?P<lane_num>[0-9]*)_R(?P<pair_num>1|2)_001\.fq\.gz
    (?P<sample_name>[^_]*)_.*_L(?P<lane_num>[0-9]*)_R(?P<pair_num>1|2)_001\.fq