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  1. IGB
  2. IGBF-3880

Investigate samtools tags consistency across datasets from Cell Ranger

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          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

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              relates to

              Task - A task that needs to be done. IGBF-3881 Add samtools filter by and color by options for CR and CB tags

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3907 Investigate adding additional Samtools tags to Filter/Color By options in IGB

              • Major - Major loss of function.
              • To-Do

              Task - A task that needs to be done. IGBF-3864 Find more single cell RNA seq datasets in10XGenomics

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese added a comment -

                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.

                Show
                nfreese Nowlan Freese added a comment - 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.
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                ann.loraine Ann Loraine added a comment -

                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.

                Show
                ann.loraine Ann Loraine added a comment - 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.
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                karthik Karthik Raveendran added a comment -

                Seems like the purpose of the ticket has been fulfilled. Moving to first level review

                Show
                karthik Karthik Raveendran added a comment - Seems like the purpose of the ticket has been fulfilled. Moving to first level review
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                karthik Karthik Raveendran added a comment - - edited

                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.

                Show
                karthik Karthik Raveendran added a comment - - edited 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 .
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                karthik Karthik Raveendran added a comment -

                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.

                Show
                karthik Karthik Raveendran added a comment - 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.

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                  • Assignee:
                    Unassigned
                    Reporter:
                    karthik Karthik Raveendran
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                    • Created:
                      Updated:
                      Resolved: