Assembly QA Part 1 DEV Steps

Welcome to the Assembly QA Part 1: DEV Steps page! 😎

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Page created Fall. 2016 by Cath, Jairo, and ChrisV.
This page is currently a draft in progress.
For now, use Releasing_an_assembly instead.

1. Set up a directory in hive

1. You will need a place to put output. Make a directory in your hive:
   1. mkdir /hive/users/cath/assemblies/assemblyName

hgwdev > hgsql -Ne "select chrom, size from chromInfo" $oldDb > oldChromSizes assemblyName (e.g., "ornAna1")
hgwdev > hgsql -Ne "select chrom, size from chromInfo" $newDb > newChromSizes assemblyName (e.g., "ornAna2")
hgwdev > sdiff -s oldChromSizes newChromSizes
mkdir /hive/users/cath/assemblies/assemblyName

1. Optional: Create an alias to your new dir

Claim it in Redmine & PushQ

1. Find your assembly in the associated Assembly Redmine ticket.
   1. If there is no Redmine for your assembly, you should create one, assign to yourself, and add the engineer as a watcher.
   2. If one exists, read carefully, assign it to yourself. Make sure the engineer is a watcher.
   3. For any issues found in the QA process, report in the Redmine ticket.
2. Find your assembly in the PushQ
   1. Click on the link in the "Queue ID" column
   2. Click the "lock" button at the top of the page to "unlock" the fields for editing.
   3. Add your name to the "Reviewer" column.

Overall Quality Check

Check chrom sizes

Ignore this if assembly is the first for a species.

For a new assembly version, compare the chrom sizes from the last assembly to this new assembly version.

Output chrom sizes into two files and compare them.

hgwdev > hgsql -Ne "select chrom, size from chromInfo" $oldDb > oldChromSizes assemblyName (e.g., "ornAna1")
hgwdev > hgsql -Ne "select chrom, size from chromInfo" $newDb > newChromSizes assemblyName (e.g., "ornAna2")
hgwdev > sdiff -s oldChromSizes newChromSizes

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🔵 Done with DEV steps? Let's go to Assembly QA Part 2: BETA Steps