andrewsparkes
commented
2 years ago Andrews notes from meeting on 14th:
HiC Meeting Notes - 13th April Attending Emma Gray, Elizabeth Cook, Alice Linsdell, Stephen Inglis, James Glover and Andrew Sparkes Background Story DPL-337 https://github.com/sanger/General-Backlog-Items/issues/176 Notes Currently around 70 Tree of Life (ToL) samples per week, numbers increasing and may double if each sample is treated to two processes. Samples are in Tubes.
Samples are tracked via google sheets. Tube manifests are sent out to ToL with sample ids and barcodes.
Google sheets track information from ToL. Information is copied into HiC schedule, another google sheet.
Capacities for both Cross-linking and Library prep (separate processes with separate capacities) are given each week to Alice (via TL in long read)
A batch of Cross-linking happens in the lab, and then the samples get put into Samples Extraction LIMs after work has been completed. A ‘stock plate’ is created in Samples Extraction LIMs.
Samples are then manually grouped together based on the number or proportion of lanes of sequencing required and genome size (Liz mentioned ranges of genome size).
A ‘fake’ Cherrypick is done as a way of re-organising the samples from the stock plate(s) into the new batch groupings on new plates. i.e. the samples are cross-linked in one grouping then re-organised for library prep and sequencing in another grouping.
A library prep and sequencing submission is created (bulk submission in Sequencescape), with a HiC library type for Novaseek sequencing.
All information is tracked in google sheets. Alice and Liz think this is not sustainable if numbers of samples increase further.
Emma G would like this work to be tracked in Traction, as opposed to Samples Extraction or Limber.
Emma G mentioned there is currently a lot of difficulty in reporting what has happened. James G mentioned that Samples Extraction has some reporting functionality that may help.
James G mentioned that it would be possible to defer pooling of samples into a sequencing batch until later in the pipeline, although this has the complication that you have to deal with tag clashes., so it may be impractical.
Emma G pointed out that the manual library prep currently being done for this work is very similar (but not identical) to the high throughput library prep being done routinely in the main labs. Is there a reason not to just push the samples through this existing library prep process?
Actions: Create a process diagram about what is currently happening and confirm with all parties that it is correct.
stevieing
Description Please can we investigate if there is additional LIMS/tracking support available for HiC tracking and submissions, to allow for a single HiC submission up-front from the SSR. Current status: Samples are received in tubes, with manifest uploaded to SS. The tubes (and the HiC protocol required) are listed on a googlesheet for the lab team. The tubes are processed through SE LIMS, which results in a stock plate ID, in SS, which is also filled back into the googlesheet by the lab team. At this point, the SSR selects samples (based on the proportion of sequencing lane required), copies these to a new googlesheet tab for tracking purposes and make the CP and library prep request in SS. We would like to reduce the tracking on googlesheets and the need for the SSR to manually select samples for batching in the middle of the process.
Potential new status: The SSR makes an up-front submission for HiC cross-linking, library prep, pooling and sequencing. The submission would allow the tissue tubes to go through SE LIMs, generate a plate and also include the lib prep and sequencing submission for HiC. This would mean that the SSR does not need to make a submission at the mid-point in the process, and a single “batch” of samples can stay together through the full lab process. If there are any alternative solutions, we would be happy to explore these. Please ensure that al13 and ad30 are also consulted on any changes to process/submissions to ensure that this fits with the lab processing.
Acceptance criteria: Not fully yet set, research story to see what is possible.
If the above suggestion is taken forward:
Who the primary contacts are for this work Liz / Emma
Knowledge or Stake holders Other people that may have specific knowledge about this work or have a stake in how it is implemented. e.g. John Smith is an expert on x
Additional context or information
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