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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Epic Link:
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Sprint:Fall 1
Description
Single cell RNA seq data has samtools tags (see link below) and ultimately we want to filter reads in IGB using these tags especially CR or CB tags, which unique IDs for cells. But first we need to know if the tags are consistent across cellranger pipeline versions and a reliable filter. The datasets in IGBF-3864 should be good enough viewed and compared for samtools tags and confirm the consistency.
https://samtools.github.io/hts-specs/SAMtags.pdf
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Assignee | Ann Loraine [ aloraine ] | Karthik Raveendran [ karthik ] |
| Description |
Single cell RNA seq data has samtools tags (see link below) and ultimately we want to filter reads in IGB using these tags especially CR or CB tags, which unique IDs for cells. But first we need to know if the tags are consistent across cellranger pipeline versions and a reliable filter. The datasets in https://samtools.github.io/hts-specs/SAMtags.pdf |
| Epic Link | IGBF-3765 [ 22984 ] |
| Sprint | Fall 1 [ 202 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Attachment | Compart samtools tags across cell ranger versions.xlsx [ 18487 ] |
| Attachment | Compart samtools tags across cell ranger versions.xlsx [ 18487 ] |
| Attachment | Compare samtools tags across cell ranger versions.xlsx [ 18488 ] |
| Attachment | Compare samtools tags across cell ranger versions.xlsx [ 18488 ] |
| Attachment | Compare samtools tags across cell ranger versions.xlsx [ 18490 ] |
| Story Points | 1 | 0.5 |
| Story Points | 0.5 | 1 |
| Assignee | Karthik Raveendran [ karthik ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Summary | Verify samtools tags consistency across datasets | Investigate samtools tags consistency across datasets from CellRanger |
| Summary | Investigate samtools tags consistency across datasets from CellRanger | Investigate samtools tags consistency across datasets from Cell Ranger |
| 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 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |