This topic describes a LabKey Server workflow for managing
samples and sequencing results generated from a PacBio Sequencer. This workflow lets you:
- import sequencing data from a PacBio Sequencer, including sample sheets, barcode identifiers, and table structures
- link sample sets and runs and organize with other information such as ids, types, tags, etc.
- keep different pool data (such as from different lanes) separate
- store multiple fastq files per barcode identifier, and accept fastq files without assuming the need for matching read counts
- browse and export the sequence files
Set Up a Dashboard
First we will set up a Genotyping dashboard, and import some sample data.
- Download pacbio.lists.zip -- This is a list archive you will import - do not unzip it.
- Create a new project of type Genotyping. Use the default settings.
- In the Lists webpart click Manage Lists.
- Click Import List Archive.
- Choose or Browse to the pacbio.lists.zip archive and click Import List Archive.
- You will see the lists imported.
- (Optional) Explore the list design of the samples list to notice that the fivemid and threemid columns are configured as lookups into the mids list.
Next, configure the necessary queries and load reference sequences:
- Click Genotyping Dashboard.
- Under Settings, click Admin.
- Under Configure Genotyping Queries, click Configure next to Runs:
- Schema = lists
- Query = runs
- View = [default View]
- Click Submit
- Click Configure next to Samples:
- Schema = lists
- Query = samples
- View = [default View]
- Click Submit.
- Click Submit again to save the query configuration.
Load some sample data: