Assembly QA Part 2 Track Steps: Difference between revisions

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====<span style="color:dodgerblue">Setup: Populate spreadsheet steps for Dev: Track Steps====
====<span style="color:dodgerblue">Setup: Populate spreadsheet steps for Dev: Track Steps====
Add the following formula to your spreadsheet to automatically populate dev steps based on each step listed as a wiki section.  
* We need to create a checklist for your assembly tracks.
:Option 1: Add "Track Steps" to your same spreadsheet, below "Dev steps"
* First, add a new tab in your spreadsheet for this.
:: You can add this formula to the same spreadsheet as your dev steps, in the next empty row after all of your dev steps. It will then populate all of the "Track Steps."
* Type in your row 1 field names:
:: Wiki Link
:: Assembly Release Steps
:: Status
:: Table 1
:: Table 2
:: Table 3
...etc


::Option 2: Add "Track Steps" to a new tab in your spreadsheet
* For "Table 1, Table 2, Table 3 (etc.) columns, you will need to add all of the tracks from your assembly.  
:: If you prefer, you can create a new tab in your spreadsheet and paste in this formula after your row 1 field names.


Formula to paste into ONE cell to populate Track Steps
Formula to paste into ONE cell to populate Track Steps

Revision as of 20:54, 8 April 2017

This page is currently a draft in progress. For now, use Releasing an assembly instead.


Navigation Menu

Home Page
Assembly QA Part 1: DEV Steps
Assembly QA Part 2: Track Steps
Assembly QA Part 3: BETA Steps
Assembly QA Part 4: RR Steps
Assembly QA Part 5: Post Release Steps


Setup: Populate spreadsheet steps for Dev: Track Steps

  • We need to create a checklist for your assembly tracks.
  • First, add a new tab in your spreadsheet for this.
  • Type in your row 1 field names:
Wiki Link
Assembly Release Steps
Status
Table 1
Table 2
Table 3

...etc

  • For "Table 1, Table 2, Table 3 (etc.) columns, you will need to add all of the tracks from your assembly.

Formula to paste into ONE cell to populate Track Steps

A2 (or the next available row in col A following your dev steps)
=HYPERLINK("http://genomewiki.ucsc.edu/genecats/index.php/Assembly_QA_Part_1:_DEV_Steps#"&SUBSTITUTE(B2," ", "_"),"link")
IMPORTANT: Drag the formula for "A" down the spreadsheet to populate the other rows.
B2 (or the next available row in col B following your dev steps)
=IMPORTXML("http://genomewiki.ucsc.edu/genecats/index.php/Assembly_QA_Part_1_DEV_Steps#", "/html/body/div/div/div/div/div/h4/span/span")

This formula will populate all the rows below it with the wiki section titles. You do no need to drag this formula down.


Dev: Run featureBits on gold/gap

Run featureBits to verify that the gold and gap tables together cover the entire genome. Run: 

 featureBits -countGaps -or $db gold gap

to make sure that the gold and gap table together cover the entire genome (should be 100%).

Example: 

featureBits -countGaps -or manPen1 gold gap
2204741241 bases of 2204741241 (100.000%) in intersection

You can run each table separately to see the coverage of each table on the genome: 

featureBits -countGaps manPen1 gold
1999066070 bases of 2204741241 (90.671%) in intersection

featureBits -countGaps manPen1 gap
205675171 bases of 2204741241 (9.329%) in intersection

Tracks Step 2



🔵 Done with TRACK steps? Go to Assembly QA Part 3: BETA Steps

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