Differences

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

--- data:illumina [2026/01/20 11:51] – "Olink" library type no longer has hyphen Richard Bowers
+++ data:illumina [2026/05/12 15:22] (current) – Addition of GEM-X Flex / OCM addition file Richard Bowers
@@ Line 61: / Line 61: @@
 === 10x Sequencing ===
-As of November 2020 we supply 10x data as a set of FASTQ files in the same manner as any other regular multiplexed library type, for both single index (SI-GA and SI-NA) and dual index (TT/NT/TN) kits. If you have received your single cell data files as compressed FASTQ files, refer to the regular sequencing section. Also refer to the section on file name conversion if these files need to be renamed for 10x downstream pipelines.
+As of November 2020 we supply 10x data as a set of FASTQ files in the same manner as any other regular multiplexed library type, for both single index (SI-GA and SI-NA) and dual index (TT/TS/TN/NT/NN) kits. If you have received your single cell data files as compressed FASTQ files, refer to the regular sequencing section. Also refer to the section on file name conversion if these files need to be renamed for 10x downstream pipelines.
 The FASTQ files you receive for SI-GA and SI-NA indexing will have all four index sequences for each barcode combined in the set of FASTQ files for the sample. A quick run through a demultiplexer will confirm the presence of the four indexes at approximately 25% of reads for each one.
@@ Line 96: / Line 96: @@
 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.
-=== 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>[<other lanes>].olink_counts.zip
-</code>
-This is a change from the early Olink runs of 2025. Please see the page [[olink|Olink Sequencing Counts]] for full details.
 ==== Supporting Files ====
@@ Line 138: / Line 128: @@
 <SLX>.<flowcell>.s_<lane>.visiuminfo.csv
 </code>
+==== 10x OCM / GEM-X Flex ====
+x On-Chip Multiplexing (OCM) and GEM-X Flex protocols are pooled after an early stage barcoding step before being pooled again for sequencing. The data as delivered is based around the latter pooling step; the same step as all other sequencing work flows go through. Thus your lane of data will be demultiplexed based only on this barcoding: the early stage indexing and pooling you will have to demultiplex yourself. However, to help with this we provide an additional file for any lane that contains libraries of these types. The file will be:
+<code>
+<SLX>.<flowcell>.s_<lane>.pooling.csv
+</code>
+This file will contain the Flex pool name (this is a name given to the first pool made in the protocol, and is pretty meaningless), the Flex number (barcode), and your sample's name, repeated for every sample in the lane.
+==== 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 ====