Assembly QA Part 2 Track Steps

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