Filename pattern
This setting is only available if the sequencer type is set to Custom.
Setting for defining the filename pattern that should be used to identify the sample ID for a given file during sample grouping (see Definition of sample grouping). The pattern should be defined as a regular expression and include a (sample-id) group in the location of the sample ID, e.g.:
- Sample ID at beginning of filename:
- Pattern:
(sample-id)_S\d+_(L\d{3}_)?R[1-2]_\d{3}\.f(ast)?q(\.gz)? - Example of matching file:
ID1234_S1_L001_R1_001.fastq.gz - Detected sample ID:
ID1234
- Pattern:
- Sample ID in middle of filename:
- Pattern:
[^_]+_(L\d+_)?(sample-id)_(R)?[1-2]\.f(ast)?q(\.gz)? - Example of matching file:
SEQRUN1_L01_ID5678_1.fq.gz - Detected sample ID:
ID5678
- Pattern:
The filename patterns used for the supported sequencer types are:
- Element Biosciences:
(sample-id)(_L\d+)?(_R[1-2])\.f(ast)?q(\.gz)?(sample-id)_S\d+_(L\d{3}_)?R[1-2]_\d{3}\.f(ast)?q(\.gz)?(sample-id)\.f(ast)?q(\.gz)?
- Illumina:
(sample-id)_S\d+_(L\d{3}_)?R[1-2]_\d{3}\.f(ast)?q(\.gz)?(sample-id)\.f(ast)?q(\.gz)?
- Ion Torrent:
(sample-id)\.u?bam(sample-id)\.f(ast)?q(\.gz)?
- MGI:
[^_]+_(L\d+_)?(sample-id)_(R)?[1-2]\.f(ast)?q(\.gz)?(sample-id)_S\d+_(L\d{3}_)?R[1-2]_\d{3}\.f(ast)?q(\.gz)?(sample-id)\.f(ast)?q(\.gz)?