CRUK-CI Genomics Help

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
data:illumina [2024/04/11 13:02] – Added Visium help Richard Bowersdata:illumina [2026/01/20 11:54] (current) – Change to Olink lane numbering Richard Bowers
Line 108: Line 108:
 We deliver with the data a report that we also use to ensure the sequencing has gone as expected. We deliver with the data a report that we also use to ensure the sequencing has gone as expected.
  
-  - Our demuliplexing and barcode balance reports. These give charts and numbers for the reads created from the sequencing. If there are indexing problems they'll show up here.+  - Our demultiplexing and barcode balance reports. These give charts and numbers for the reads created from the sequencing. If there are indexing problems they'll show up here.
   - Our single cell reports. These are only present for 10x single cell lanes and are produced per sample.   - Our single cell reports. These are only present for 10x single cell lanes and are produced per sample.
   - [[https://www.bioinformatics.babraham.ac.uk/projects/fastqc|FastQC]]: Assorted sequencing metrics. Where the lane is regular paired end sequencing, there will be a FastQC report for each read (FastQC is not a tool that handles paired end).   - [[https://www.bioinformatics.babraham.ac.uk/projects/fastqc|FastQC]]: Assorted sequencing metrics. Where the lane is regular paired end sequencing, there will be a FastQC report for each read (FastQC is not a tool that handles paired end).
Line 128: Line 128:
 <SLX>.<flowcell>.s_<lane>.visiuminfo.csv <SLX>.<flowcell>.s_<lane>.visiuminfo.csv
 </code> </code>
 +
 +==== Olink Sequencing ====
 +
 +If the ''Library Type'' of your library is "''Olink''" we will run the program //ngs2counts// on each Olink lane to get the counts across the flowcell for all lanes containing the same SLX pool. The additional file produced will be:
 +
 +<code>
 +<SLX>.<flowcell>.s_<lane>.olink_counts.zip
 +</code>
 +
 +The lane number will be the lowest lane number in which the SLX pool was sequenced, though the counts will be for all lanes containing that pool.
 +
 +This is a change from the early Olink runs of 2025. Please see the page [[olink|Olink Sequencing Counts]] for full details.
  
 ==== File Name Conversion ==== ==== File Name Conversion ====
  
-Some tools require the FASTQ files to be named as they would be when delivered by //BCL Convert//, not as we provide them. 10x's pipelines are a notable example. To this end, the script [[https://genomicsequencing.cruk.cam.ac.uk/sequencing/resources/crukci_to_illumina.py|crukci_to_illumina.py]] will convert a directory containing our FASTQ files to names as they would have been immediately after //BCL Convert//.+Some tools require the FASTQ files to be named as they would be when delivered by //BCL Convert//, not as we provide them. 10x's pipelines are a notable example. To this end, the script [[https://genomicshelp.cruk.cam.ac.uk/tools/crukci_to_illumina.py|crukci_to_illumina.py]] will convert a directory containing our FASTQ files to names as they would have been immediately after //BCL Convert//.
  
 It changes our file names to the pattern: It changes our file names to the pattern: