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  1. IGB
  2. IGBF-3466

Add SL4 and SL5 salmon.merged.gene_counts.tsv for 30-605730043 to repository

        Details

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

          Description

          Repository pistil-rna-seq lacks "counts" files for data set 30-605730043 even though multiqc_report and _samples.csv files are present.

          For this task, add these two files to pistil-rna-seq/ExternalData:

          • 30-605730043_SL4_salmon.merged.gene_counts.tsv
          • 30-605730043_SL5_salmon.merged.gene_counts.tsv

          using naming convention:

          [data set]_[assembly]_salmon.merged.gene_counts.tsv

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              ann.loraine Ann Loraine created issue -
              ann.loraine Ann Loraine made changes -
              Field Original Value New Value
              Epic Link IGBF-3251 [ 22132 ]
              Mdavis4290 Molly Davis made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
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              Mdavis4290 Molly Davis added a comment -

              Branch: https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3466

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              Mdavis4290 Molly Davis added a comment - Branch : https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3466
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              Mdavis4290 Molly Davis added a comment -

              PR: https://bitbucket.org/hotpollen/pistil-rna-seq/pull-requests/11

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              Mdavis4290 Molly Davis added a comment - PR : https://bitbucket.org/hotpollen/pistil-rna-seq/pull-requests/11
              Mdavis4290 Molly Davis made changes -
              Assignee Molly Davis [ molly ]
              Mdavis4290 Molly Davis made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              Mdavis4290 Molly Davis made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              Mdavis4290 Molly Davis made changes -
              Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
              Mdavis4290 Molly Davis made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              Mdavis4290 Molly Davis made changes -
              Assignee Ann Loraine [ aloraine ]
              ann.loraine Ann Loraine made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
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              ann.loraine Ann Loraine added a comment -

              Testing by checking number of lines per file after pulling main to my local.

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              ann.loraine Ann Loraine added a comment - Testing by checking number of lines per file after pulling main to my local.
              ann.loraine Ann Loraine made changes -
              Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
              ann.loraine Ann Loraine made changes -
              Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
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              ann.loraine Ann Loraine added a comment - - edited

              Tested with:

              local aloraine$ wc -l 30-605730043_SL4_salmon.merged.gene_counts.tsv
   34076 30-605730043_SL4_salmon.merged.gene_counts.tsv
local aloraine$ wc -l 30-804059537_SL4_salmon.merged.gene_counts.tsv
   34076 30-804059537_SL4_salmon.merged.gene_counts.tsv

              and

              local aloraine$ wc -l 30-605730043_SL5_salmon.merged.gene_counts.tsv
   36649 30-605730043_SL5_salmon.merged.gene_counts.tsv
local aloraine$ wc -l 30-804059537_SL5_salmon.merged.gene_counts.tsv 
   36649 30-804059537_SL5_salmon.merged.gene_counts.tsv

              As shown above, the new data files for 30-605730043 have the same number of lines as their SL4 and SL5 counterparts from the 30-804059537 dataset. Also, the SL5 files have more lines than the SL4 files, which is consistent with prior knowledge that the SL5 assembly has more gene models in it.

              Sanity check passes. Moving to DONE.

              Show
              ann.loraine Ann Loraine added a comment - - edited Tested with: local aloraine$ wc -l 30-605730043_SL4_salmon.merged.gene_counts.tsv 34076 30-605730043_SL4_salmon.merged.gene_counts.tsv local aloraine$ wc -l 30-804059537_SL4_salmon.merged.gene_counts.tsv 34076 30-804059537_SL4_salmon.merged.gene_counts.tsv and local aloraine$ wc -l 30-605730043_SL5_salmon.merged.gene_counts.tsv 36649 30-605730043_SL5_salmon.merged.gene_counts.tsv local aloraine$ wc -l 30-804059537_SL5_salmon.merged.gene_counts.tsv 36649 30-804059537_SL5_salmon.merged.gene_counts.tsv As shown above, the new data files for 30-605730043 have the same number of lines as their SL4 and SL5 counterparts from the 30-804059537 dataset. Also, the SL5 files have more lines than the SL4 files, which is consistent with prior knowledge that the SL5 assembly has more gene models in it. Sanity check passes. Moving to DONE.
              ann.loraine Ann Loraine made changes -
              Resolution Done [ 10000 ]
              Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
              ann.loraine Ann Loraine made changes -
              Story Points 0.5 0.25

                People

                • Assignee:
                  Mdavis4290 Molly Davis
                  Reporter:
                  ann.loraine Ann Loraine
                • Votes:
                  0 Vote for this issue
                  Watchers:
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                  Dates

                  • Created:
                    Updated:
                    Resolved: