Differences

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--- submission:colourbalance [2024/12/02 10:10] – Creation and first draft Richard Bowers
+++ submission:colourbalance [2026/05/01 11:02] (current) – [Illumina's Documentation] Johanna Barbieri
@@ Line 10: / Line 10: @@
   - [[https://knowledge.illumina.com/instrumentation/novaseq-6000/instrumentation-novaseq-6000-reference_material-list/000001931|NovaSeq 6000]]
-We recommend you read these guides to understand the issues involved. Illumina also provide a document "[[https://support-docs.illumina.com/SHARE/IndexAdaptersPooling/Content/SHARE/FrontPages/IndexAdapterPooling.htm|Index Adapters Pooling Guide]]" that gives a fuller read of the subject.
+We recommend you read these guides to understand the issues involved. Illumina also provide a document  [[https://emea.support.illumina.com/downloads/index-adapters-pooling-guide-1000000041074.html|"Index Adapters Pooling Guide"]]that gives a fuller read of the subject.
 ===== The Colour Balance Tool =====
@@ Line 23: / Line 23: @@
 You need to submit sequences of the same length: it will not be able to analyse a mix of shorter and longer indexes.
+==== A note about old style 10x indexes ====
+// This section is relevant for the single index, four barcodes per sample 10x systems, namely SIGA and SINA. //
+If you submit a file with SIGA or SINA index labels, or a CSV with four columns, the tool will automatically convert these into single indexes with four times the number of barcodes. This is because these kits apply four single indexes to every sample, so each one of them adds to the combination of the single index read.
+For example, if you submit a file containing:
+<code>
+SINAA1
+SINAA2
+ACGTACGT,CGTACGTA,GTACGTAC,TACGTACG
+</code>
+the index combination is:
+<code>
+AAACGGCG
+CCTACCAT
+GGCGTTTC
+TTGTAAGA
+AGCCCTTT
+CAAGTCCA
+GTGAGAAG
+TCTTAGGC
+ACGTACGT
+CGTACGTA
+GTACGTAC
+TACGTACG
+</code>
+These are the four sequences of the first label plus the four sequences of the second label and the four sequences provided just as sequences. You will see in the text area on the page this has happened as well as a plot with eight i7 sequences.