Differences

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--- data:illumina [2024/04/10 14:07] – Created with text from the original page, updated for BCL Convert Richard Bowers
+++ data:illumina [2026/01/20 11:54] (current) – Change to Olink lane numbering Richard Bowers
@@ Line 1: / Line 1: @@
-====== Files Resulting from Illumina Sequencing ======
+====== Illumina Sequencing Data Files ======
 Your sequencing data will made available in the standard FASTQ file format. We also provide some smaller files giving information about those files, and a report for each lane of sequencing.
@@ Line 108: / Line 108: @@
 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.
   - [[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 114: / Line 114: @@
 This report will be named ''<SLX>.<flowcell>.s_<lane>.html''.
+==== 10x Visium Data ====
+If any of your samples have been through the 10x CytAssist as part of the Visium work flow you will receive the image files alongside your sequencing data. They will be fetched automatically by the download tool (CRUK-CI researchers) or will be put into your FTP directory (external users). The CytAssist image file follows the naming convention:
+<code>
+<SLX>.<barcode>.<flowcell>.s_<lane>.cytassist.tif
+</code>
+There is an additional information file produced for Visium containing sample information (name and barcode label) together with our Visium identifier for each sample, the slide identifiers and the position on the slides.
+<code>
+<SLX>.<flowcell>.s_<lane>.visiuminfo.csv
+</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 ====
-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: