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==== | ||
* 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 | 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.
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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