Assembly QA Part 1 DEV Steps

This page is currently a draft in progress. For now, use Releasing_an_assembly instead.

Navigation Menu 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

Dev 1.0. Set up a directory in hive

You will need a place to put output during the QA/Release process. The use of the "hive" directory is encouraged as the best location because of ample space.

Dev 1.1. Make a directory in your hive

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

Dev 1.2. Optional: Create an alias to your new dir

When you add an alias from your .bashrc file, you can simply type that alias in your command line as a shortcut to the associated command. To do this, follow the steps below:

1. cd (go to your home directory on hgwdev)
2. confirm the location of .bashrc. type "ls -a" in your home directory to see all hidden files that have a " . " in the filename. This way you can confirm the location of your .bashrc file.
3. open the file for editing. If you're using the vi editor, you can type "vi .bashrc" to edit the file. Add an alias by typing in the line below:

alias hive='cd /hive/users/yourUserName/assemblies/yourAssembly'

For example,

alias hive='cd /hive/users/cath/assemblies/manPen1'

Dev 2.0: 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.

Dev 3.0. Check chrom sizes

Dev 3.1. List step 1 here

Dev 3.2. List step 2 here

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

=Dev 4.0. Are associated alignment files (listed in the pushQ) to valid assemblies on the RR?

Dev 4.1. List step 1 here

Dev 4.2. List step 2 here

chain/net/liftOver CATH TO EDIT

Dev.3: Check "minimal browser" criteria: got required tracks?

Visit this page for the required tracks to be considered a minimal browser.

Add this later as a QA step

Assemblies/sequences, from various organizations, are submitted to the mother ship GenBank.
Those assemblies might be included in RefSeq if criteria are met.

The QA check should be to go out to NCBI and double check that the accessionID is correct

RefSeq assemblies:

use accession ID: GCF_000002315.4 (e.g., galGal5)

are delivered with chrMt (if they exisit)

are delivered with NCBI gene predictions

Genbank assemblies:

use accession ID: GCA_000001305.2

delivered without a chrMt.

do not have gene predictions.

For the UCSC Genome Browser, it is preferable to use RefSeq assemblies (in part due to 'more data'). This is a "learn as we go" direction; historically GeneBank was preferred.

Helpful article: Nature, 2012 A beginner's guide to eukaryotic genome annotation

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