Assembly QA Part 1 DEV Steps

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

Home: Assembly_Release_QA_Steps Assembly QA Part 1: DEV Steps Assembly QA Part 2: BETA Steps Assembly QA Part 3: RR Steps Assembly QA Part 4: Post Release Steps

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

Dev.1: Set up a directory in hive

• You will need a place to put output. Make a directory in your hive:

mkdir /hive/users/userName/assemblies/assemblyName  e.g.:  mkdir /hive/users/cath/assemblies/manPen1

• Optional: Create an alias to your new dir

Dev.2: 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.
   4. Press the "Submit" button to save your edits.

Overall Quality Check

Check chrom sizes

CHRIS V TO EDIT

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. You are not checking annotations on the reference sequence, you are just checking the number of base pairs per chrom/contig, and making sure that nothing has changed drastically (i.e., millions of base pairs different). Also take a look for general differences, such as chrom labels or number of chrom/contigs.

Output chrom sizes into two files, sort each file by using the command below

Compare the sorted files

Add note about viewing http://genome.ucsc.edu/cgi-bin/hgGateway and clicking on "View Sequences" button - bring up 2 windows side by side

hgwdev > hgsql -Ne "select chrom, size from chromInfo" $oldDb > oldChromSizes assemblyName (e.g., "panTro4")
hgwdev > hgsql -Ne "select chrom, size from chromInfo" $newDb > newChromSizes assemblyName (e.g., "panTro5")
hgwdev > sdiff -s oldChromSizes newChromSizes

=Check that any chain/net/liftOvers listed in the pushQ are to valid assemblies on the RR (batches)

CATH TO EDIT

Verify that there are enough tracks to be considered at least a "minimal" browser

JAIRO TO EDIT

.

.

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