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  1. IGB
  2. IGBF-3346

Prepping data and entries for SRA for Muday time course

        Details

        • Type: Task
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          2
        • Epic Link:
        • Sprint:
          Summer 2 2023 May 29, Summer 3 2023 June 12, Summer 6 2023 July 24, Summer 7 2023 Aug 7

          Description

          Starting the data prepping and table prepping for the Muday time course data.

          EXTRA step will be needed due to the labelling errors!!

          A script to rename the files will be needed and this script will need review to ensure we get that step right!

          Otherwise, the SRA submission should be straightforward, similar to IGBF-3255.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3406 Re-run Nextflow Muday time course data with SL5 data downloaded from SRA

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3290 Use new sample labels recommended by Muday Lab

              • 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

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                28 older comments
                Hide
                Permalink
                robofjoy Robert Reid added a comment -

                We need to add all of the Accession IDs before we close this out!

                Stay tuned.

                Show
                robofjoy Robert Reid added a comment - We need to add all of the Accession IDs before we close this out! Stay tuned.
                Hide
                Permalink
                robofjoy Robert Reid added a comment - - edited

                SRR Accesions:
                SRR25478240
                SRR25478241
                SRR25478242
                SRR25478243
                SRR25478244
                SRR25478245
                SRR25478246
                SRR25478247
                SRR25478248
                SRR25478249
                SRR25478250
                SRR25478251
                SRR25478252
                SRR25478253
                SRR25478254
                SRR25478255
                SRR25478256
                SRR25478257
                SRR25478258
                SRR25478260
                SRR25478261
                SRR25478262
                SRR25478263
                SRR25478264
                SRR25478265
                SRR25478266
                SRR25478267
                SRR25478268
                SRR25478269
                SRR25478270
                SRR25478272
                SRR25478273
                SRR25478275
                SRR25478276
                SRR25478277
                SRR25478278
                SRR25478279
                SRR25478280
                SRR25478281
                SRR25478282
                SRR25478283
                SRR25478284
                SRR25478285
                SRR25478286
                SRR25478287
                SRR25478289
                SRR25478290
                SRR25478291
                SRR25478292
                SRR25478293
                SRR25478294
                SRR25478295
                SRR25478296
                SRR25478297
                SRR25478298
                SRR25478299
                SRR25478300
                SRR25478301
                SRR25478302
                SRR25478304
                SRR25478305
                SRR25478306
                SRR25478307
                SRR25478308
                SRR25478309
                SRR25478310
                SRR25478311
                SRR25478259
                SRR25478271
                SRR25478274
                SRR25478303
                SRR25478288

                Show
                robofjoy Robert Reid added a comment - - edited SRR Accesions: SRR25478240 SRR25478241 SRR25478242 SRR25478243 SRR25478244 SRR25478245 SRR25478246 SRR25478247 SRR25478248 SRR25478249 SRR25478250 SRR25478251 SRR25478252 SRR25478253 SRR25478254 SRR25478255 SRR25478256 SRR25478257 SRR25478258 SRR25478260 SRR25478261 SRR25478262 SRR25478263 SRR25478264 SRR25478265 SRR25478266 SRR25478267 SRR25478268 SRR25478269 SRR25478270 SRR25478272 SRR25478273 SRR25478275 SRR25478276 SRR25478277 SRR25478278 SRR25478279 SRR25478280 SRR25478281 SRR25478282 SRR25478283 SRR25478284 SRR25478285 SRR25478286 SRR25478287 SRR25478289 SRR25478290 SRR25478291 SRR25478292 SRR25478293 SRR25478294 SRR25478295 SRR25478296 SRR25478297 SRR25478298 SRR25478299 SRR25478300 SRR25478301 SRR25478302 SRR25478304 SRR25478305 SRR25478306 SRR25478307 SRR25478308 SRR25478309 SRR25478310 SRR25478311 SRR25478259 SRR25478271 SRR25478274 SRR25478303 SRR25478288
                Hide
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                Mdavis4290 Molly Davis added a comment -

                [~RobertReid] Hi Dr. Reid, I was wondering why the SRR names are the same as seedling and mature pollen submission IGBF-3347. Is that correct, because then I would only need to rerun the data once for one ticket. Let me know!

                Show
                Mdavis4290 Molly Davis added a comment - [~RobertReid] Hi Dr. Reid, I was wondering why the SRR names are the same as seedling and mature pollen submission IGBF-3347. Is that correct, because then I would only need to rerun the data once for one ticket. Let me know!
                Hide
                Permalink
                robofjoy Robert Reid added a comment -

                For the SRA dataset SRP441343, both sets of data are contained therein. (Muday's and the mature pollen/seedling)

                https://trace.ncbi.nlm.nih.gov/Traces/?view=study&acc=SRP441343

                NCBi forced me to combine them due to the similarities.
                There are 126 total. 72 of those are Muday's time course.

                Is this what you were looking for?

                Show
                robofjoy Robert Reid added a comment - For the SRA dataset SRP441343, both sets of data are contained therein. (Muday's and the mature pollen/seedling) https://trace.ncbi.nlm.nih.gov/Traces/?view=study&acc=SRP441343 NCBi forced me to combine them due to the similarities. There are 126 total. 72 of those are Muday's time course. Is this what you were looking for?
                Hide
                Permalink
                Mdavis4290 Molly Davis added a comment - - edited

                Ok! I have the 72 Muday SRR names but you pasted the same 72 in seedling and mature pollen experiment IGBF-3347 and was wondering what those names are actually supposed to be? Thank you for your help! [~RobertReid]

                Show
                Mdavis4290 Molly Davis added a comment - - edited Ok! I have the 72 Muday SRR names but you pasted the same 72 in seedling and mature pollen experiment IGBF-3347 and was wondering what those names are actually supposed to be? Thank you for your help! [~RobertReid]

                  People

                  • Assignee:
                    robofjoy Robert Reid
                    Reporter:
                    robofjoy Robert Reid
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                    • Created:
                      Updated: