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
Situation: Spoke with Matt Sergent (msergent@illumina.com) who is the local area rep for Charlotte. He said he is frequently on campus if we had questions. He mentioned that Illumina works differently in how they label each cell, and that they are not using UMI values. It's unclear if that means the BAM file will have the samtool tag for the cell barcode (CB/CR?).
I also asked if Illumina had example RNA-Seq data we could look at. He gave me one link (fluentbio) and Karthik found another.
https://www.fluentbio.com/species-mixture-experiment-with-large-cell-input/
https://help.ica.illumina.com/project/p-cohorts/cohorts-publicdata
Task: Find an example BAM file created using Illumina's single cell RNA-Seq pipeline and look to see if it has the CB/CR tags like the 10X genomics file.
Attachments
Issue Links
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-3765 [ 22984 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Security | Hidden [ 10001 ] |
| Sprint | Fall 1 [ 202 ] |
Looking into datasets in Human Cell atlas: https://explore.data.humancellatlas.org/projects
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Fall 1 [ 202 ] | Fall 1, Fall 2 [ 202, 203 ] |
| Rank | Ranked higher |
| Sprint | Fall 1, Fall 2 [ 202, 203 ] | Fall 1 [ 202 ] |
Follow-up: We started using 10X Genomics data files they provide from their data sets web site. See single cell RNA-Seq Quickload https://bitbucket.org/lorainelab/scrna-seq
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| 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 ] |
Karthik also found this link on the Illumina samtools tags which includes the BC tag: 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
UPDATE: The files available from Fluent are limited to the FASTQ files, which would require significant time to run through various pipelines. I've sent them an email asking if they had BAM files available and will update when/if I hear back.
Illumina's BaseSpace says they have BAM files, but when we try to download them the download fails, as they are using some proprietary download software (the files are not publicly available, they require an account through BaseSpace).