When trying to replicate the process using data from this paper, there are three fastq files present per sample, each with content in both the @ and + sequence description lines.
When running the pipeline for the example data with the same version of Cutadapt in the readme, it generates an error: "cutadapt: error: At line 3: Sequence descriptions in the FASTQ file don't match. The second sequence description must be either empty or equal to the first description."
In the European archive for the same sample however, there are only two fastq files where in both the second sequence description line is empty. While this would remedy the sequence description error, the script is now looking for three fastqs instead of two and throwing an error. Is there a workaround for this issue?
When trying to replicate the process using data from this paper, there are three fastq files present per sample, each with content in both the @ and + sequence description lines.
When running the pipeline for the example data with the same version of Cutadapt in the readme, it generates an error: "cutadapt: error: At line 3: Sequence descriptions in the FASTQ file don't match. The second sequence description must be either empty or equal to the first description."
In the European archive for the same sample however, there are only two fastq files where in both the second sequence description line is empty. While this would remedy the sequence description error, the script is now looking for three fastqs instead of two and throwing an error. Is there a workaround for this issue?