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  1. IGB
  2. IGBF-3163

Rename or create symbolic links to BAM alignments files to remove "sorted" in the file names

        Details

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

          Description

          The alignment 'BAM' files all contained the word "sorted" in their names.

          Let's rename these files without the "sorted" string to reduce cognitive load. Let's only use the SRR name as the prefix.

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              Task - A task that needs to be done. IGBF-3162 Generate scaled coverage graphs for RNA-Seq alignments

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Link This issue blocks IGBF-3162 [ IGBF-3162 ]
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                Mdavis4290 Molly Davis added a comment - - edited

                The following was completed with the use of the 'mv' command to remove the word 'sorted'
                from each bam file.

                Directories:
                /nobackup/tomato_genome/alt_splicing/SRP252265/results/star_salmon

                /nobackup/tomato_genome/alt_splicing/SRP328042-molly/results/star_salmon

                Show
                Mdavis4290 Molly Davis added a comment - - edited The following was completed with the use of the 'mv' command to remove the word 'sorted' from each bam file. Directories: /nobackup/tomato_genome/alt_splicing/SRP252265/results/star_salmon /nobackup/tomato_genome/alt_splicing/SRP328042-molly/results/star_salmon
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
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                ann.loraine Ann Loraine added a comment -

                Improvement request:

                The indexes also need to be renamed, e.g.,

                • SRR15111738.sorted.bam.bai

                needs to be renamed to:

                • SRR15111738.bam.bai

                attn: [~molly]

                Show
                ann.loraine Ann Loraine added a comment - Improvement request: The indexes also need to be renamed, e.g., SRR15111738.sorted.bam.bai needs to be renamed to: SRR15111738.bam.bai attn: [~molly]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Assignee Molly Davis [ molly ]
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                Mdavis4290 Molly Davis added a comment -

                Just finished fixing the bam.bai files to not contain the word 'sorted' as well.

                [~aloraine]

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                Mdavis4290 Molly Davis added a comment - Just finished fixing the bam.bai files to not contain the word 'sorted' as well. [~aloraine]
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                ann.loraine Ann Loraine added a comment -

                Confirmed: Indexes files are renamed.
                Moving to Done.

                Show
                ann.loraine Ann Loraine added a comment - Confirmed: Indexes files are renamed. Moving to Done.
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                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 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: