Details
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Type:
New Feature
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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: None
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Labels:
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Story Points:4
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Epic Link:
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Sprint:Spring 2019 Sprint 1, Spring 2019 Sprint 2
Description
Write a python program that accepts data from Ensembl BioMart and from UCSC Table Browser EnsGene table and produces bed14 format file.
- Field 4 contains Ensembl transcript id (e.g., ENSCSAT00000001292.1)
- Field 13 contains Ensembl gene id for the transcript (e.g., ENSCSAG00000003267.1) from BioMart
- Field 14 contains descriptive information from BioMart
The key work of this script is to cross-reference gene ids and functional descriptions obtained from BioMart with transcript ids obtained from UCSC Genome Browser.
We developed this so that we could include vervet (African green monkey) gene annotations in IGB Quickload, a user request.
Attachments
Issue Links
- relates to
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IGBF-1401 Add Chlorocebus sabaeus ("green monkey") to IGB quickload
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1395 [ 17470 ] |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Open [ 1 ] |
| Sprint | Spring 2019 Sprint 1 [ 59 ] | Spring 2019 Sprint 1, Spring 2019 Sprint 2 [ 59, 60 ] |
| Rank | Ranked higher |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Jill Jenkins [ jill ] |
| Status | Pull Request Submitted [ 10101 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | Open [ 1 ] |
| Assignee | Jill Jenkins [ jill ] |
| Description |
Write a python program that accepts data from Ensembl BioMart and from UCSC Table Browser EnsGene table and produces bed14 format file.
* Field 4 contains Ensembl transcript id (e.g., ENSCSAT00000001292.1) * Field 13 contains Ensembl gene id for the transcript (e.g., ENSCSAG00000003267.1) from BioMart * Field 14 contains descriptive information from BioMart The key work of this script is to cross-reference gene ids and functional descriptions obtained from BioMart with transcript ids obtained from UCSC Genome Browser. We developed this so that we could include vervet (African green monkey) gene annotations in IGB Quickload, a user request. |
Write a python program that accepts data from Ensembl BioMart and from UCSC Table Browser EnsGene table and produces bed14 format file.
* Field 4 contains Ensembl transcript id (e.g., ENSCSAT00000001292.1) * Field 13 contains Ensembl gene id for the transcript (e.g., ENSCSAG00000003267.1) from BioMart * Field 14 contains descriptive information from BioMart The key work of this script is to cross-reference gene ids and functional descriptions obtained from BioMart with transcript ids obtained from UCSC Genome Browser. We developed this so that we could include vervet (African green monkey) gene annotations in IGB Quickload, a user request. |
| Status | Open [ 1 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Jill Jenkins [ jill ] |
| Resolution | Done [ 10000 ] | |
| Status | Pull Request Submitted [ 10101 ] | Closed [ 6 ] |
| Assignee | Jill Jenkins [ jill ] |
| Workflow | Loraine Lab Workflow [ 18238 ] | Fall 2019 Workflow Update [ 20014 ] |
| Workflow | Fall 2019 Workflow Update [ 20014 ] | Revised Fall 2019 Workflow Update [ 22141 ] |