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--- submission:barcodesearch [2025/02/10 09:07] – removed - external edit (Unknown date) 127.0.0.1
+++ submission:barcodesearch [2025/02/10 09:07] (current) – ↷ Page name changed from submission:index_kit_and_barcode_look_up_search to submission:barcodesearch Ania Piskorz
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+======= Index Kit and Barcode Look Up =======
+This tool allows one to find barcodes in our sequencing system from given
+sequences of bases. It should assist in selecting the corrent barcodes for
+your submission forms, or highlight that we may need to add a new index
+type and set of barcodes.
+[[https://genomicsequencing.cruk.cam.ac.uk/sequencing/tools/BarcodeLookup.action|The tool is part of the submission portal]].
+The tool is a simple look up of sequences to find any barcodes that match.
+This is an exact match: it will only find barcodes of the same length and
+sequence. It will not return, for example, a six base sequence within the
+sequence of an eight base index. It does not do "near" matching, where there
+is a difference in one or more bases.
+The tool supports single and dual index. In the latter case, the sequences
+should be separated by a single hyphen ("-"). The search will automatically
+cope try to find matches with the reverse complement of the second index,
+as this is a common cause of confusion. All our barcode sequences are in
+our system in the forward direction, with our post-sequencing processing
+automatically creating the reverse complement when required.
+One does not have to provide all barcodes of the same length and type for
+a search. This set would all be valid to search for at once:
+<code>
+ACGTCA
+ATGGTCAT
+GTCATGAA-TGCTAGTA
+ATGTCA-TAGCTACG
+</code>
+//I have not checked if these actually match any of our barcodes! It is just for example.//
+===== Using the Tool =====
+Simply copy and paste your sequences, one per line, into the text box and
+click the "update" button. The tool will perform its search and return the
+results as a table giving every barcode each sequence can be found in.
+The table will show each (valid) sequence in the order submitted, together
+with the label of the barcode it is found in and the barcode category
+(index type) it belongs to.
+If the search matches a barcode with the reverse complement in index two,
+the barcode name is highlighted in bold.
+An example:
+^ Sequence ^ Category ^ Barcode (CRUK-CI name) ^
+| ''TTCTACATAC-CTAACTGTAA'' | CSgenetics | CSg-24 |
+| ::: | IDT for Illumina DNA/RNA UD Indexes | idtUDP0024 |
+| ::: | Illumina DNA/RNA UD Indexes | IlluminaUDP0024 |
+| ::: | Illumina Nextera UDIs 96 | UDP0024 |
+| ''AACGTCTG-GCGTCATT'' | ABclonal-UDI | ABclonalUDI67 |
+| ::: | IDT Xgen UDIs | xGenUDI67 |
+| ::: | IDT Xgen UDIs with UMI | xGenUDI67-UMI |
+| ''AACGTCTG-AATGACGC'' | ABclonal-UDI | **ABclonalUDI67** |
+| ::: | IDT Xgen UDIs | **xGenUDI67** |
+| ::: | IDT Xgen UDIs with UMI | **xGenUDI67-UMI** |
+Note that the sequences ''AACGTCTG-GCGTCATT'' and ''AACGTCTG-AATGACGC'' are
+effectively the same, just with index two having the reverse complement.
+This is why the same barcodes are found for two different sequences.
+==== 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. //
+These barcodes, where there are four sequences per sample that are all individual i7 indexes, are searched for any one of the four barcodes: you will be able to find the barcode with any one of the individual sequences used by that barcode. You should not enter four barcodes on a line, as this will locate nothing.