Details
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Type:
Task
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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:None
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Story Points:1
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Sprint:Summer 7
Description
IGB can now open and display contents of CRAM files distributed by Nebula Genomics.
AL has a recently downloaded CRAM file from Nebula that would be great to use, but it's huge - around 84 Gb.
For this task, let's use a command line tool to extract the data for chromosome 1, the chromosome shows by default when it opens the latest human genome available in the browser - hg38.
Let's deploy the actual data file on RENCI hosting and add it as a new data set in IGB Quickload main.
Once it is there, we can then create a tutorial and also a video showing how to open and load the reads to look for or sanity-check polymorphisms. The tutorial ought to explain the soft clips and the SNPs - what they are and how to interpret them. The materials could also explain how to visually check some of the SNP calls on the Nebula Web site.
Attachments
Issue Links
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- To-Do
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2809 [ 19325 ] |
| Description |
IGB can now open and display contents of CRAM files distributed by Nebula Genomics.
AL has a recently downloaded CRAM file from Nebula that would be great to use, but it's huge - around 84 Gb. For this task, let's use a command line tool to extract the data for chromosome 1, the chromosome shows by default when it opens the latest human genome available in the browser - hg38. Let's deploy the actual data file on RENCI hosting and add it as a new data set in IGB Quickload main. Once it is there, we can then create a tutorial and also a video showing how to open and load the reads to look for or sanity-check polymorphisms. The tutorial ought to explain the soft clips and the SNPs - what they are and how to interpret them. The materials should also explain how to visually check some of the SNP calls on the Nebula Web site. |
IGB can now open and display contents of CRAM files distributed by Nebula Genomics.
AL has a recently downloaded CRAM file from Nebula that would be great to use, but it's huge - around 84 Gb. For this task, let's use a command line tool to extract the data for chromosome 1, the chromosome shows by default when it opens the latest human genome available in the browser - hg38. Let's deploy the actual data file on RENCI hosting and add it as a new data set in IGB Quickload main. Once it is there, we can then create a tutorial and also a video showing how to open and load the reads to look for or sanity-check polymorphisms. The tutorial ought to explain the soft clips and the SNPs - what they are and how to interpret them. The materials could also explain how to visually check some of the SNP calls on the Nebula Web site. |
| Summary | Set up data for human genome sequencing / CRAM demo | Deploy new NEBULA data for human genome sequencing / CRAM demo |
| Link | This issue blocks IGBF-3854 [ IGBF-3854 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Attachment | M1YNF4X1J.header_section.txt [ 18475 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Epic Link | IGBF-2809 [ 19325 ] | IGBF-3856 [ 23155 ] |
| Attachment | 2024-08-22-InterestingSoftClipPattern-2.png [ 18476 ] | |
| Attachment | 2024-08-22-InterestingSoftClipPattern.png [ 18477 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] | Paige Kulzer [ pkulzer ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Paige Kulzer [ pkulzer ] | Ann Loraine [ aloraine ] |
| 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 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |