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  1. IGB
  2. IGBF-4045

NEXTFLOW using TSA contigs as reference, using raw reads as input

        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

          GOAL: Another NEXTFLOW run using the TSA contigs as the reference.
          We use the reads of Kelsies just like the original expt.

          1. get NEXTFLOW to run
          2. Summarize the alignments

          Once this is done, we make a new ticket and start DESEQ2 * 4 varieties and compare time points and overall general patterns if there are any.

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              robofjoy Robert Reid added a comment -

              I looked through and I see all of the bam files and salmon count tables.

              We are good to move on to ticket #IGBF-4052, deseq on the read counts!!

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              robofjoy Robert Reid added a comment - I looked through and I see all of the bam files and salmon count tables. We are good to move on to ticket # IGBF-4052 , deseq on the read counts!!
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              bbendick Brandon Bendickson added a comment -

              Nextflow completed for all 4 varieties without error. Results of the 4 nextflow runs are found here: /projects/tomato_genome/fnb/dataprocessing/brandon_work/FCS-FILTER-NEXTFLOW

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              bbendick Brandon Bendickson added a comment - Nextflow completed for all 4 varieties without error. Results of the 4 nextflow runs are found here: /projects/tomato_genome/fnb/dataprocessing/brandon_work/FCS-FILTER-NEXTFLOW
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              bbendick Brandon Bendickson added a comment -

              Yes, will continue and run for rest of the varieties

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              bbendick Brandon Bendickson added a comment - Yes, will continue and run for rest of the varieties
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              robofjoy Robert Reid added a comment -

              Great!!
              Does this needs repeating for the other 3 varieties?

              R

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              robofjoy Robert Reid added a comment - Great!! Does this needs repeating for the other 3 varieties? R
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              bbendick Brandon Bendickson added a comment -

              Heinz run using TSA contigs as reference has completed without error. Results and files are located in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/FCS-FILTER-NEXTFLOW/Hei_1

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              bbendick Brandon Bendickson added a comment - Heinz run using TSA contigs as reference has completed without error. Results and files are located in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/FCS-FILTER-NEXTFLOW/Hei_1

                People

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