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
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Summary | Add blacklist genes to human genome in IGB | Add blacklist genes to IGB |
| Description |
"blacklist" genes are genes or regions in the human genome that give bizarre results in sequence-based assays.
Let's include these in IGB. See: https://www.nature.com/articles/s41598-019-45839-z and https://www.biostars.org/p/171354/#:~:text=Here%2C%20we%20define%20the%20ENCODE,of%20cell%20line%20or%20experiment. For a visualization, also see: * https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3477-y * https://tarpan.shinyapps.io/tarpan/ (click "blacklist" option) |
"blacklist" genes are genes or regions in a genome that give bizarre results in sequence-based assays.
Let's include these in IGB. References: * https://www.nature.com/articles/s41598-019-45839-z * Visualizations: * Tarpan: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3477-y * Tarpan: https://tarpan.shinyapps.io/tarpan/ (click "blacklist" option) |
| Sprint | Fall 7 Dec 14 - Dec 23 [ 110 ] | Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 110, 111 ] |
| Rank | Ranked higher |
| Summary | Add blacklist genes to IGB | Add blacklist genes to IGB quickload for mouse, human, fruit fly |
| Summary | Add blacklist genes to IGB quickload for mouse, human, fruit fly | Add blacklist regions to IGB quickload for mouse, human, fruit fly |
| Description |
"blacklist" genes are genes or regions in a genome that give bizarre results in sequence-based assays.
Let's include these in IGB. References: * https://www.nature.com/articles/s41598-019-45839-z * Visualizations: * Tarpan: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3477-y * Tarpan: https://tarpan.shinyapps.io/tarpan/ (click "blacklist" option) |
"blacklist" genes are genes or regions in a genome that give bizarre results in sequence-based assays.
Let's include these in IGB. References: * https://www.nature.com/articles/s41598-019-45839-z Visualizations: * Tarpan: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3477-y * Tarpan: https://tarpan.shinyapps.io/tarpan/ (click "blacklist" option) |
| Comment |
[ This github repo directory contains bed files with blacklisted regions:
* https://github.com/Boyle-Lab/Blacklist/tree/master/lists ] |
| Description |
"blacklist" genes are genes or regions in a genome that give bizarre results in sequence-based assays.
Let's include these in IGB. References: * https://www.nature.com/articles/s41598-019-45839-z Visualizations: * Tarpan: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3477-y * Tarpan: https://tarpan.shinyapps.io/tarpan/ (click "blacklist" option) |
"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: * https://github.com/Boyle-Lab/Blacklist/tree/master/lists References: * https://www.nature.com/articles/s41598-019-45839-z Visualizations: * Tarpan: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3477-y * Tarpan: https://tarpan.shinyapps.io/tarpan/ (click "blacklist" option) |
| Sprint | Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8 [ 110, 111 ] | Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22 [ 110, 111, 112 ] |
| Rank | Ranked higher |
| Sprint | Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22 [ 110, 111, 112 ] | Fall 7 Dec 14 - Dec 23, Winter 1 Dec 28 - Jan 8, Winter 2 Jan 11 - Jan 22, Winter 3 Jan 25 - Feb 5 [ 110, 111, 112, 113 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| 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 [ 110, 111, 112, 113 ] | 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 [ 110, 111, 112, 113, 114 ] |
| Rank | Ranked higher |
| 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 [ 110, 111, 112, 113, 114 ] | 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 [ 110, 111, 112, 113, 114, 115 ] |
| Rank | Ranked higher |
| Assignee | Philip Badzuh [ pbadzuh ] |
Please use genome_src repository to place code used for this.
| 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 [ 110, 111, 112, 113, 114, 115 ] | 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, Winter 6 Mar 8 - Mar 19 [ 110, 111, 112, 113, 114, 115, 116 ] |
| Rank | Ranked higher |
| Assignee | Philip Badzuh [ pbadzuh ] |
| 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, Winter 6 Mar 8 - Mar 19 [ 110, 111, 112, 113, 114, 115, 116 ] | 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 [ 110, 111, 112, 113, 114, 115 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Assignee | Nowlan Freese [ nfreese ] |
| 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 [ 110, 111, 112, 113, 114, 115 ] | 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 [ 110, 111, 112, 113, 114, 115, 122 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| 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 [ 110, 111, 112, 113, 114, 115, 122 ] | 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 [ 110, 111, 112, 113, 114, 115, 122, 123 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| 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 [ 110, 111, 112, 113, 114, 115, 122, 123 ] | 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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124 ] |
| Rank | Ranked higher |
| 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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124 ] | 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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125 ] |
| Rank | Ranked higher |
| 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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125 ] | 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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125, 126 ] |
| Rank | Ranked higher |
| 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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125, 126 ] | 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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125, 126, 127 ] |
| Rank | Ranked higher |
| 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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125, 126, 127 ] | 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 - Aug 10 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125, 126, 127, 128 ] |
| Rank | Ranked higher |
| 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 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125, 126, 127, 128 ] | 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 2021Sep 13 - Sep 24 [ 110, 111, 112, 113, 114, 115, 122, 123, 124, 125, 126, 127, 128, 129 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Nowlan Freese [ nfreese ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
[~aloraine] - do we want to store the files in IGB Quickload?
| Attachment | blacklist_v2.zip [ 16782 ] |
Replying to previous comment: Yes, alongside gene annotations. When you commit to svn, please include ticket number in the commit message (for future reference).
| Attachment | blacklist_v2.zip [ 16782 ] |
I have been unable to identify specific patch versions for the blacklist genomes. There is a file for each genome with metadata, but it only lists the assembly without the patch information. From reading this description on patches, they do not affect chromosome coordinates, so the patch version should not have any effect on the blacklist regions.
Heads up in case you are on Mac and update to Big Sur, SVN is not officially supported but can be installed through HomeBrew.
[~aloraine] - I think I found a discrepancy in the naming of one of the Drosophila genomes.
UCSC lists the Drosophila Aug. 2014 assembly as dm6.
igbquickload.org/quickload has D_melanogaster_Jul_2014 as a genome version.
Synonyms.txt lists D_melanogaster_Aug_2014 as being the dm6 assembly.
Looking at the flybase site, it is unclear precisely what date is correct. NCBI lists the same date of release (August 2014) as UCSC for dm6. NCBI states that "The gene annotation is based on Release 6.32 provided by FlyBase." The file in igbquickload.org is 6.03.
Any thoughts on this would be appreciated. I would assume that various versions of dm6 contain the same chromosome coordinates, so the blacklist should be applicable to any version of dm6. I could add the blacklist file to D_melanogaster_Jul_2014. We may want to then update the synonyms.txt to point to D_melanogaster_Jul_2014 for dm6, so that the UCSC data can also be loaded.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] | Nowlan Freese [ nfreese ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Nowlan Freese [ nfreese ] |
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.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
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
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Nowlan Freese [ nfreese ] |
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.
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Attachment | 2696.txt [ 16784 ] |
| Fix Version/s | 9.1.10 Major Release [ 10700 ] |
| Issue Type | Task [ 3 ] | New Feature [ 2 ] |
| Issue Type | New Feature [ 2 ] | Updated Genome [ 11 ] |
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.