Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3683

Update SRA to use the correct sample codes for Muday lab time course data

        Details

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

          Description

          As shown in the linked ticket, we discovered that 16 samples from the Muday lab's flavonoid time course data were assigned incorrect sample codes.

          We decided to update those records in the SRA to use the correct sample codes.

          Robert Reid is working on that.

            Attachments

              Issue Links

              is blocked by

              Task - A task that needs to be done. IGBF-3701 Muday time course: Check first sequences in renamed fastq VS. what is in SRA

              • Minor - Minor loss of function, or other problem where easy workaround is present.
              • Closed
              relates to

              Task - A task that needs to be done. IGBF-3720 Re-run Nextflow Muday time course data again with SL5 and data downloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3727 Create new input file for checking SRA code

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3596 Compare original Muday flavonoid data to SRA Re-run data

              • Major - Major loss of function.
              • Closed

                Activity

                Descending order - Click to sort in ascending order
                Hide
                Permalink
                Mdavis4290 Molly Davis added a comment -

                Review: I use the Run selector for SRP460750 on NCBI to check the newly re-annotated runs. I will review each of the 16 that needed to be re-annoted based on the check SRA markdown created.

                • SRR25478288 was re-annotated with sample code V.34.30.9
                • SRR25478289 was re-annotated with sample code V.28.30.9
                • SRR25478291 was re-annotated with sample code V.34.15.9
                • SRR25478292 was re-annotated with sample code V.28.15.9
                • SRR25478276 was re-annotated with sample code V.34.75.9
                • SRR25478277 was re-annotated with sample code V.28.75.9
                • SRR25478278 was re-annotated with sample code V.34.45.9
                • SRR25478279 was re-annotated with sample code V.28.45.9
                • SRR25478272 was re-annotated with sample code F.34.30.9
                • SRR25478273 was re-annotated with sample code F.28.30.9
                • SRR25478274 was re-annotated with sample code F.34.15.9
                • SRR25478275 was re-annotated with sample code F.28.15.9
                • SRR25478259 was re-annotated with sample code F.34.75.9
                • SRR25478260 was re-annotated with sample code F.28.75.9
                • SRR25478261 was re-annotated with sample code F.34.45.9
                • SRR25478262 was re-annotated with sample code F.28.45.9

                After checking each of the samples that need to be re-annotated on SRA I see no problem with the data. Assigning ticket back to Dr. Reid to finalize and move to done! Then Once this ticket is closed new tickets can be made to rerun the new re-annotated data through the pipeline again.

                Show
                Mdavis4290 Molly Davis added a comment - Review : I use the Run selector for SRP460750 on NCBI to check the newly re-annotated runs. I will review each of the 16 that needed to be re-annoted based on the check SRA markdown created. SRR25478288 was re-annotated with sample code V.34.30.9 SRR25478289 was re-annotated with sample code V.28.30.9 SRR25478291 was re-annotated with sample code V.34.15.9 SRR25478292 was re-annotated with sample code V.28.15.9 SRR25478276 was re-annotated with sample code V.34.75.9 SRR25478277 was re-annotated with sample code V.28.75.9 SRR25478278 was re-annotated with sample code V.34.45.9 SRR25478279 was re-annotated with sample code V.28.45.9 SRR25478272 was re-annotated with sample code F.34.30.9 SRR25478273 was re-annotated with sample code F.28.30.9 SRR25478274 was re-annotated with sample code F.34.15.9 SRR25478275 was re-annotated with sample code F.28.15.9 SRR25478259 was re-annotated with sample code F.34.75.9 SRR25478260 was re-annotated with sample code F.28.75.9 SRR25478261 was re-annotated with sample code F.34.45.9 SRR25478262 was re-annotated with sample code F.28.45.9 After checking each of the samples that need to be re-annotated on SRA I see no problem with the data. Assigning ticket back to Dr. Reid to finalize and move to done! Then Once this ticket is closed new tickets can be made to rerun the new re-annotated data through the pipeline again.
                Hide
                Permalink
                robofjoy Robert Reid added a comment -

                Changes made!
                Time to review if all changes have truly been made.

                For review:

                Check the SRA and its various tables to see if there are any of the mislabels in there.

                Show
                robofjoy Robert Reid added a comment - Changes made! Time to review if all changes have truly been made. For review: Check the SRA and its various tables to see if there are any of the mislabels in there.
                Hide
                Permalink
                robofjoy Robert Reid added a comment -

                PRJNA1017816-changes2Biosample-reAssignSRR.xlsx

                I have sent them what I think is a simple excel sheet highlighting these differences at the Biosample level.
                We will see how they respond.
                R

                Show
                robofjoy Robert Reid added a comment - PRJNA1017816-changes2Biosample-reAssignSRR.xlsx I have sent them what I think is a simple excel sheet highlighting these differences at the Biosample level. We will see how they respond. R
                Hide
                Permalink
                robofjoy Robert Reid added a comment -

                Apparently we do not contact the SRA people. The SRA data is correct.
                We need to contact the Biosample people. biosamplehelp@ncbi.nlm.nih.gov

                I will ping them and request the changes, as I cannot edit that metatable directly.

                Rob

                Show
                robofjoy Robert Reid added a comment - Apparently we do not contact the SRA people. The SRA data is correct. We need to contact the Biosample people. biosamplehelp@ncbi.nlm.nih.gov I will ping them and request the changes, as I cannot edit that metatable directly. Rob
                Hide
                Permalink
                robofjoy Robert Reid added a comment -

                Uhoh, that will get trickier.
                Those columns are not editable via the manage data tabs.

                I will send an email to the SRA to get the Replicate code and library name columns to be in sync with Sample name column.

                Rob

                Show
                robofjoy Robert Reid added a comment - Uhoh, that will get trickier. Those columns are not editable via the manage data tabs. I will send an email to the SRA to get the Replicate code and library name columns to be in sync with Sample name column. Rob
                6 older comments

                  People

                  • Assignee:
                    robofjoy Robert Reid
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: