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  1. IGB
  2. IGBF-4417

Improve single-cell RNA-Seq repository even more

        Details

        • Type: Task
        • Status: In Progress (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
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          Description

          I am working on making the exciting and amazing new single cell RNA-Seq Quickload repository easier to work with by making the titles and descriptions of the annots.xml files more descriptive and useful.

          My process:

          • Add the repository as a local folder after cloning it from the git repository at https://bitbucket.org/lorainelab/scrna-seq
          • Load a genome version
          • Click on the existing data sets URL linkout icons.
          • Observe the title, sub-title and first lines of "Data Set Overview"
          • Copy title as title into annots.xml for the dataset as "title" into annots.xml
          • Copy subtitle + first line (or lines, if info looks extra useful!) into annots.xml as "description" attribute
          • Make a note of any interesting data sets we can add!

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              ann.loraine Ann Loraine created issue -
              ann.loraine Ann Loraine made changes -
              Field Original Value New Value
              Epic Link IGBF-1765 [ 17855 ]
              ann.loraine Ann Loraine made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              ann.loraine Ann Loraine made changes -
              Sprint Spring 3 [ 235 ] Spring 3, Summer 2026 [ 235, 236 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
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              ann.loraine Ann Loraine added a comment - - edited

              To test:

              • Add single cell RNA-Seq Quickload following instructions at https://bitbucket.org/lorainelab/scrna-seq
              • Open H_sapiens_Dec_2013
              • Make a note of the number of sequences listed in Current Genome tab (595 as of May 2026)
              • Open scRNA-Seq quickload folder in Available Data sectoin of Data Access tab
              • Click on each checkbox to load data set, make sure that the data can load
              • Check if the number of sequences in the Current Genome tab changed (might happen if BAM file used a different human genome build). If that happened, click on a BAM alignment file and look at the CL attribute to see if you can figure out what genome build was used in the alignment process
              • Follow the link-out to the corresponding page on the 10X Genomics Web site. Check that title and description match what's on the page as described above
              • Once the data set is loaded into a new track, select its track label and then open the Selection Info tag. The name of the loaded file will appear in the "file URL" field. Check that it matches what is shown on the 10X Web page under the tab labeled "Output and supplemental files". Tip: you can easily test by copying the URL from the BAM file link and then trying File > Open URL. IGB will copy the URL into the box. When you proceed with trying to add it, IGB will show a warning letting you know if you have already added that particular URL. If that happens, and if that URL has already been added as you did just now, you can rest assured that the URLs are the same.
              Show
              ann.loraine Ann Loraine added a comment - - edited To test: Add single cell RNA-Seq Quickload following instructions at https://bitbucket.org/lorainelab/scrna-seq Open H_sapiens_Dec_2013 Make a note of the number of sequences listed in Current Genome tab (595 as of May 2026) Open scRNA-Seq quickload folder in Available Data sectoin of Data Access tab Click on each checkbox to load data set, make sure that the data can load Check if the number of sequences in the Current Genome tab changed (might happen if BAM file used a different human genome build). If that happened, click on a BAM alignment file and look at the CL attribute to see if you can figure out what genome build was used in the alignment process Follow the link-out to the corresponding page on the 10X Genomics Web site. Check that title and description match what's on the page as described above Once the data set is loaded into a new track, select its track label and then open the Selection Info tag. The name of the loaded file will appear in the "file URL" field. Check that it matches what is shown on the 10X Web page under the tab labeled "Output and supplemental files". Tip: you can easily test by copying the URL from the BAM file link and then trying File > Open URL. IGB will copy the URL into the box. When you proceed with trying to add it, IGB will show a warning letting you know if you have already added that particular URL. If that happens, and if that URL has already been added as you did just now, you can rest assured that the URLs are the same.
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              ann.loraine Ann Loraine added a comment - - edited

              Checked H_sapiens_Dec_2013 as per above criteria. No problems noticed except for one:

              After loading BAM files, number of sequences in Current Genome panel increased to 764.

              Show
              ann.loraine Ann Loraine added a comment - - edited Checked H_sapiens_Dec_2013 as per above criteria. No problems noticed except for one: After loading BAM files, number of sequences in Current Genome panel increased to 764.
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              ann.loraine Ann Loraine added a comment -

              Interesting genes to look at:

              • HNRNPL - expressed in PBMCs, has two alternative promoters, proximal promoter most apparent in scRNA-Seq data
              Show
              ann.loraine Ann Loraine added a comment - Interesting genes to look at: HNRNPL - expressed in PBMCs, has two alternative promoters, proximal promoter most apparent in scRNA-Seq data
              ann.loraine Ann Loraine made changes -
              Comment [ Need to use links to our own runs of Rasha's data in the S_lycopersicum_Jun_2022 data, hosted on CyVerse. ]

                People

                • Assignee:
                  ann.loraine Ann Loraine
                  Reporter:
                  ann.loraine Ann Loraine
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                  • Created:
                    Updated: