Details
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Type:
Updated Genome
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 9.1.10 Major Release
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Labels:None
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Story Points:1.5
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Epic Link:
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Sprint:Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5, Winter 4 Feb 8 - Feb 19, Winter 5 Feb 22 - Mar 5, Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25, Summer 2 2021 Jun 28 - Jul 9, Summer 3 2021 Jul 12 - Jul 23, Summer 4 2021 Aug 2 - Aug 13, Fall 1 2021 Aug 16 - Aug 27, Fall 2 2021 Aug 30 - Sep10, Fall 3 2021 Sep 13 - Sep 24
Description
"blacklist" genes are genes or regions in a genome that give bizarre results in sequence-based assays.
Let's include these in IGB.
This github repo directory contains bed files with blacklisted regions:
References:
Visualizations:
- Tarpan: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3477-y
- Tarpan: https://tarpan.shinyapps.io/tarpan/ (click "blacklist" option)
Attachments
Issue Links
Activity
All of the blacklist files have been pushed to the SVN repository, with the exception of dm6.
I have created IGBF-2955 to address pushing the changes to the SciDas and Quickload servers.
Please don't test until sites are updated and deployed. (Sorry - I moved this forward to "ready for testing" prematurely.)
Now it is ready for testing.
attn: Nowlan Freese
Discrepancy - While testing I noticed that in the C_elegans_oct_2010 (ce10) genome the blacklist region was outside of the range of some of the chromosomes (i.e. the blacklist regions were greater than the max chromosome size). The genome length in IGB (C_elegans_oct_2010) is correct when compared to UCSC. I also re-downloaded the ce10 blacklist file. It appears that the locations of some of the blacklist regions are incorrect or mis-annotated, indicating an issue with the pipeline that the blacklist authors used.
Testing complete, no issues.
Closing ticket.
To show these in IGB:
The regions are probably simple spans with chromosome name, start, and end position, and maybe a strand indicator. When users select and load data from the file with blacklist regions, they should see the name of the region displayed.