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tutorial-detailed-libraries.md

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Libraries tutorial
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[Download the PDF]({{ '/presentations/miso_libraries.pdf' | prepend: site.baseurl }})

Table of Contents
  1. Logging In
  2. Propagating aliquots to libraries
  3. Receiving Libraries
  4. Adding Library QCs
  5. Propagating libraries to dilutions
  6. Scanning libraries into your outbox
  7. Propagating libraries to library aliquots
  8. Creating pool orders
  9. Creating Pools
  10. Ordering sequencing
  11. Troubleshooting
Print the worksheet for this section here: Libraries Worksheet.

{% include logging_in.md detailed=page.is-detailed %}

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2. Propagating aliquots to libraries

A library is made from one sample for a single target platform and has a specific design associated with it that decides the selection and strategies used to make the library. A library may also have indices (primers/sequencing barcodes/molecular IDs) and QC information.

MISO stores two important pieces of information about how a library was generated: the selection (e.g., PCR, cDNA) and the strategy (e.g., WGS, WXS, amplicon). A design captures both a selection and strategy and the list of allowed designs is limited based on the sample type (e.g., a cDNA sample can only have SM, WT, or MR library designs and these lock the selection and strategy type accordingly).

2.0 Scan aliquots into your inbox

First, we accept the aliquots made by the samples team and put them into your inbox.

{% include inboxes.md %}

{% include libraries-from-samples.md detailed=page.is-detailed %}

2.2 Bulk propagate aliquots to libraries from Box page

In this section, you will use the aliquots created already and create libraries. These libraries can be sorted based on the parent sample's location within the box, and indices can be added based on the box position.

  1. On the Boxes page, find your box and click on its link.
  2. Select all the aliquots in your box by control-clicking all the aliquots in the box (command-click on a Mac). If the aliquots are all in one row or column, you can click on the row/column header to select all items in that row or column. Use control-click (or command-click) to select more than one row or column.
  3. Click the Propagate button at the top left of the box contents table. If the top left of the box contents table indicates that more than one type of element is selected, de-select the non-aliquot tubes and then click Propagate.
  4. In the dialog that appears, choose 1 replicate. If necessary, choose to propagate to Library.
  5. Click Propagate.
  6. Click the Sort button at the top of the table.
  7. In the dialog that appears, choose Sample Location (by rows) as the Primary Sort. Leave all other options at their default values.
  8. Click Sort. The libraries you are creating are now sorted based on their parent sample's position within the box. Sorting can be done by rows (A01, A02, B01, B02, ...) or columns (A01, B01, A02, B02, ...).
    • This may be useful when using the Sciclone robot to create libraries and add indices at a particular plate location. Once the libraries are sorted based on the parent sample's location, the indices can be copy-pasted in the same order that the robot requires.
  9. Do not save these libraries.

{% include libraries-receipt.md detailed=page.is-detailed section=3 platform=site.platform_type type=site.library_type %}

3.2 Receipt Transfers

{% include receipt-transfer.md detailed=page.is-detailed items_exercise="3.1" type="library" type_plural="libraries" %}

{% include libraries-qc.md %}

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5. Scanning libraries into your outbox

{% include outboxes.md %}

{% include libraries-to-library-aliquots.md detailed=page.is-detailed %}

{% include libraries-pool-orders.md detailed=page.is-detailed %}

{% include libraries-library-aliquots-to-pools.md detailed=page.is-detailed %}

{% include libraries-orders.md %}

{% include libraries-trouble.md %}

What if I assign a library to the wrong parent aliquot?

You can delete the library and re-create it. If this is not appropriate because the library is already included in a sequencer run, please {{ site.miso_admin_contact }} to get assistance from {{ site.miso_admin }}.

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