CRUK-CI Genomics Help

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support:demultiplexing [2025/08/06 09:09] – Help on multiple indexes per file Richard Bowerssupport:demultiplexing [2025/08/06 09:10] (current) – Richard Bowers
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 The data files the CRUK-CI sequencing service provides after sequencing your samples are demultiplexed according to the barcodes provided in the submission spreadsheet. It sometimes happens that users of the service make a mistake when filling in this spreadsheet and put an incorrect index against one or more samples, or samples are omitted from the submission spreadsheet. This manifests as those samples' FASTQ files being much smaller than one might expect, or not present at all. The data files the CRUK-CI sequencing service provides after sequencing your samples are demultiplexed according to the barcodes provided in the submission spreadsheet. It sometimes happens that users of the service make a mistake when filling in this spreadsheet and put an incorrect index against one or more samples, or samples are omitted from the submission spreadsheet. This manifests as those samples' FASTQ files being much smaller than one might expect, or not present at all.
  
-The good news is that the reads are still present in the data: they've just not been allocated to the sample. There is a file for each lane of sequencing called SLX-????.<flow cell id>.s_?.r_?.lostreads.fq.gz that contains all the reads that could not be allocated to any of the indexes listed in the submission spreadsheet.+The good news is that the reads are still present in the data: they've just not been allocated to the sample. There is a file for each lane of sequencing called ''SLX-????.<flow cell id>.s_?.r_?.lostreads.fq.gz'' that contains all the reads that could not be allocated to any of the indexes listed in the submission spreadsheet.
  
 The bad news is that correcting the submission information regarding the indexes attached to the samples is troublesome to the point of impossibility in our Clarity LIMS system. We cannot therefore fix your submission to rerun demultiplexing and attach those files so you can fetch them with the download tool or on the FTP site. Rerunning demultiplexing is also not an automatic process: a little time and effort will be needed to reprocess the FASTQ files. The bad news is that correcting the submission information regarding the indexes attached to the samples is troublesome to the point of impossibility in our Clarity LIMS system. We cannot therefore fix your submission to rerun demultiplexing and attach those files so you can fetch them with the download tool or on the FTP site. Rerunning demultiplexing is also not an automatic process: a little time and effort will be needed to reprocess the FASTQ files.
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-The example here are for single index, but dual index works in exactly the same way with the additional column for the i5 sequence.+The examples here are for single index, but dual index works in exactly the same way with the additional column for the i5 sequence.
  
 ===== Running the Demultiplexer ===== ===== Running the Demultiplexer =====