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 ] |
Adding link to 10xGenomics Cell Ranger Barcoded BAM Tags for reference: https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-outputs-bam
Adding link to Illumina BAM file tag reference: https://support.illumina.com/help/BaseSpace_App_RNA_Amplicon_v1_OLH_1000000042465/Content/Source/Informatics/BAM-Format_swBS_appDNAA_appRNAA.htm#:~:text=end%20alignment%20quality.-,%E2%80%A2,or%20the%20UCSC%20Genome%20Browser.
| Story Points | 1 | 0.5 |
| Story Points | 0.5 | 1 |
Seems like the purpose of the ticket has been fulfilled. Moving to first level review
| Assignee | Karthik Raveendran [ karthik ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Title change suggestion:
"Investigate samtools tags consistency across datasets"
instead of
"Verify samtools tags consistency across datasets"
Then it will be clear from the title that no conclusion about veracity is possible yet, but work happened that might be useful to readers.
| 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 |
I updated the title of the ticket based on Dr. Loraine's suggestion. I also added that the datasets analyzed in this ticket are all from/processed with Cell Ranger.
I reviewed the excel sheet with Karthik.
Closing ticket.
| 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 ] |
See Excel attached to this ticket. CB and CR is the samtools tags we are interested in because CR is the unique cell barcode and CB is cell identifier. These two tags are consistently available in the all 4 versions of cell ranger we checked.