CRUK-CI Genomics Help

Differences

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

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
submission:slx_submissions [2026/01/08 13:27] – [Submission Guidelines] Johanna Barbierisubmission:slx_submissions [2026/08/04 15:15] (current) – [Submission Guidelines] Johanna Barbieri
Line 20: Line 20:
   -  If you are submitting for unspecified indexing where you will demultiplex yourself, you must specify the **index lengths** required for each index. _We cannot accept your library unless we have this information_.   -  If you are submitting for unspecified indexing where you will demultiplex yourself, you must specify the **index lengths** required for each index. _We cannot accept your library unless we have this information_.
   -  Enter the average library length including insert and adapters (see point 4 of further information).   -  Enter the average library length including insert and adapters (see point 4 of further information).
-  -  Select required option for **custom primers**. See the custom primers guide for more information.+  -  Select required option for **custom primers**. See the**[[customprimers| custom primers guide]]** for more information.
   -  Select **sample type, sample source and species** from the drop down menus.   -  Select **sample type, sample source and species** from the drop down menus.
   -  Complete **billing information**. This is critical for correct invoicing: please follow the popup instructions in the field. Only enter a **PO number** if applicable to your department or organisation. **Leave PO number blank if it does not apply!** Resist the temptation to put "N/A" or "None": it will complicate your bills.   -  Complete **billing information**. This is critical for correct invoicing: please follow the popup instructions in the field. Only enter a **PO number** if applicable to your department or organisation. **Leave PO number blank if it does not apply!** Resist the temptation to put "N/A" or "None": it will complicate your bills.
Line 32: Line 32:
            * **Index** must be the corresponding Index Name (e.g. i701_i501) rather than the index sequence. Some index types are grouped (for instance all Nextera kits as they all use the same original set of Illumina Nextera index sequence), so as long as the sequence matches your index sequence you are able to submit using that index name.            * **Index** must be the corresponding Index Name (e.g. i701_i501) rather than the index sequence. Some index types are grouped (for instance all Nextera kits as they all use the same original set of Illumina Nextera index sequence), so as long as the sequence matches your index sequence you are able to submit using that index name.
            * **Species** is only needed if you have a mix of species in the pool. Use this field to assign a species for any sample whose species differs from that set in cell C25 (the species common across the pool).            * **Species** is only needed if you have a mix of species in the pool. Use this field to assign a species for any sample whose species differs from that set in cell C25 (the species common across the pool).
-  - For a pool with no indexing, inline barcodes or unspecified indexing, complete a single row for the whole pool; i.e. a pool of six libraries is still only one row in the sample information table. The index should read //"None"// for no index, //"INLINE"// for inline barcodes and //"Unspecified Index"// for custom indexing. As noted in point 2, the number of samples in pool should be set to 1.+  - For a pool with no indexing, inline barcodes or unspecified indexing, complete a single row for the whole pool; i.e. a pool of six libraries is still only one row in the sample information table. The index should read //"No Index"// for no index, //"INLINE"// for inline barcodes and //"Unspecified Index"// for custom indexing. As noted in point 2, the number of samples in pool should be set to 1.
  
 A full list of the supported indexes can be found on the index information page. If your index type is not currently supported, email the genomics helpdesk to enquire if the new indexes could be added. We cannot add every available index, but we will add to our list if there is a significant requirement for new indexing kits or options. A full list of the supported indexes can be found on the index information page. If your index type is not currently supported, email the genomics helpdesk to enquire if the new indexes could be added. We cannot add every available index, but we will add to our list if there is a significant requirement for new indexing kits or options.
Line 39: Line 39:
 ==== Make the Submission ==== ==== Make the Submission ====
  
-  - Run your completed submission form through this submission application. Any errors will be reported back to you for correction. If there are no errors, you will be asked to confirm your submission to the Genomics' LIMS system.+  - **Run your completed submission form through this [[https://genomicsequencing.cruk.cam.ac.uk/sequencing/submit/UploadSubmission.action|submission application]]. Any errors will be reported back to you for correction. If there are no errors, you will be asked to confirm your submission to the Genomics' LIMS system.**
   - Once your submission is complete, bring your SLX tube(s) to Genomics lab 026 or the Cambridge Institute reception for our external collaborators. Reception can accept tubes between 09:30-16:30 Monday to Friday.   - Once your submission is complete, bring your SLX tube(s) to Genomics lab 026 or the Cambridge Institute reception for our external collaborators. Reception can accept tubes between 09:30-16:30 Monday to Friday.
  
Line 50: Line 50:
   - If you must submit a pool with two or more different barcoding kits used in it, please submit with Index Type set to "Unspecified (Other)". The pool can be sequenced to your requirements but it is wholly your responsibility to demultiplex the FASTQ files you will receive. The sequencing service does not support demultiplexing such pools.   - If you must submit a pool with two or more different barcoding kits used in it, please submit with Index Type set to "Unspecified (Other)". The pool can be sequenced to your requirements but it is wholly your responsibility to demultiplex the FASTQ files you will receive. The sequencing service does not support demultiplexing such pools.
   - If you submit a sample for **multiple lanes** of NovaSeq X, **__we strongly suggest running a MiSeq i100__** to help us optimise loading on the instrument. Failing that, __we can't guaranty optimal results__.   - If you submit a sample for **multiple lanes** of NovaSeq X, **__we strongly suggest running a MiSeq i100__** to help us optimise loading on the instrument. Failing that, __we can't guaranty optimal results__.
 +  - Please bear in mind that the size of sequencing data can be very large (especially for multiple lanes of NovaSeq X 25B). Make sure you have enough space set aside to download the data.
  
  
Line 56: Line 57:
            * MiSeq: 15µl of your pooled library at 10-20nM.            * MiSeq: 15µl of your pooled library at 10-20nM.
            * NextSeq: 15µl of your pooled library at 10-20nM.            * NextSeq: 15µl of your pooled library at 10-20nM.
-           * MiSeq Express: 15µl at 4nM precisely.+           * MiSeq Express or NextSeq Express: 15µl at 4nM precisely.
            * NovaSeq submissions dependent upon flowcell type:            * NovaSeq submissions dependent upon flowcell type:
  
Line 66: Line 67:
 |NovaSeq X 25B | 5-10nM |30µl | |NovaSeq X 25B | 5-10nM |30µl |
  
-There is no standard workflow available, like on the NovaSeq 6000, only “Xp”.+Please do not submit molarities above 50nM.
  
 ==== Yields ==== ==== Yields ====