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  1. IGB
  2. IGBF-4223

Make table of Gene lengths

        Details

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

          Description

          Take SL4 CDS file and create a new table that contains just 2 columns

          The SOLYID
          The gene length

          Read in each fasta, Calculate the length of the sequence.

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              Task - A task that needs to be done. IGBF-4220 Normalize Salmon Counts

              • Major - Major loss of function.
              • Closed

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                robofjoy Robert Reid added a comment -

                The table produces decimal points.
                Many of them.
                Like a boat load.
                Too many.

                Can we add a step prior to writing to file to floor each number in table to 2 decimal points ?

                The reason is I am getting a

                Error: vector memory limit of 32.0 Gb reached, see mem.maxVSize()

                I bet the decimals are the cause.

                Show
                robofjoy Robert Reid added a comment - The table produces decimal points. Many of them. Like a boat load. Too many. Can we add a step prior to writing to file to floor each number in table to 2 decimal points ? The reason is I am getting a Error: vector memory limit of 32.0 Gb reached, see mem.maxVSize() I bet the decimals are the cause.
                Hide
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                robofjoy Robert Reid added a comment -

                Decimals were not the cause.
                Rob's Rstudio no like it, specifically spmething about tidyverse.

                When I read it using read.delim, all is well.

                So this table is not the issue.

                Show
                robofjoy Robert Reid added a comment - Decimals were not the cause. Rob's Rstudio no like it, specifically spmething about tidyverse. When I read it using read.delim, all is well. So this table is not the issue.

                  People

                  • Assignee:
                    bbendick Brandon Bendickson
                    Reporter:
                    robofjoy Robert Reid
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                    Dates

                    • Created:
                      Updated:
                      Resolved: