Assembly QA Part 2 Track Steps: Difference between revisions
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====<span style="color:dodgerblue"> | ====<span style="color:dodgerblue">Dev: Run featureBits on gold/gap==== | ||
</span> | </span> | ||
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: | |||
<pre> | |||
featureBits -countGaps -or manPen1 gold gap | |||
2204741241 bases of 2204741241 (100.000%) in intersection | |||
</pre> | |||
You can run each table separately to see the coverage of each table on the genome: | |||
<pre> | |||
featureBits -countGaps manPen1 gold | |||
1999066070 bases of 2204741241 (90.671%) in intersection | |||
featureBits -countGaps manPen1 gap | |||
205675171 bases of 2204741241 (9.329%) in intersection | |||
</pre> | |||
====<span style="color:dodgerblue">Tracks Step 2==== | ====<span style="color:dodgerblue">Tracks Step 2==== |
Revision as of 20:38, 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
Add the following formula to your spreadsheet to automatically populate dev steps based on each step listed as a wiki section.
- Options:
- 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."
- If you prefer, you can create a new tab in your spreadsheet and paste in this formula after your row 1 field names:
- 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