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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:
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          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

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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

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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
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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]

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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]
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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.

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                ann.loraine Ann Loraine added a comment - Confirmed: Indexes files are renamed. Moving to Done.

                  People

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

                    • Created:
                      Updated:
                      Resolved: