- First check the both short reads files are present in the folder and both files are readable. If both are true, please check the next section.
- Read files are paired based on the Illumina naming conventions. If a non-default filename convention is used or there are multiple file pairs that match the same pattern, a fallback pairing method is initiated. This method assumes that filenames within a pair differ in a single character (e.g. sample1_1.fastq,gz and sample_1_2.fastq.gz). If file pairing is not successful, both files in a pair will show up as single data. In this case, please rename the relevant files.
