Differences

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

--- data:illumina [2025/12/19 13:29] – Note about the combine-olink GitHub repository. Richard Bowers
+++ data:illumina [2026/01/20 11:54] (current) – Change to Olink lane numbering Richard Bowers
@@ Line 97: / Line 97: @@
 The sample number (the second part of the file name, "S5" etc) is an internal sample number generated by //BCL Convert// that has no significance.
-=== O-link Sequencing ===
-If the ''Library Type'' of your library is "''O-link''" we will run the program //ngs2counts// on each O-link lane to get the counts for that lane. The additional files produced will be:
-<code>
-<SLX>.<flowcell>.s_<lane>.olink_counts.csv
-<SLX>.<flowcell>.s_<lane>.olink_meta.json
-</code>
-If you need to combine counts across lanes, we have written a Python script to combine one or more counts CSV and meta JSON files into a single pair that contain the sum of the counts in the individual files. This can be found in the GitHub repository https://github.com/crukci-bioinformatics/combine-olink
 ==== Supporting Files ====
@@ Line 138: / Line 128: @@
 <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 ====