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  1. IGB
  2. IGBF-3901

Rerun RNA-Spades on Nagcarlang

        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; Checking to see if nagcarlang's rna-spades run was complete. We will run this job again in a new folder from scratch.

          And then compare these results to previous ones.

          Comparing total # of hits in the FNA files and the sequence lengths.

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              robofjoy Robert Reid added a comment -

              Steps in this task:

              1. Re run Nag through RNA-Quast
              2. Blat to SL5 again to assign id's to the de novo contigs
              3. Count how many SL5 matches did we get? Should be 25K +.
              4. Run script to assign the soly IDs.
              5. Run Next FLow using these contigs and SL5 as the reference.
              Show
              robofjoy Robert Reid added a comment - Steps in this task: Re run Nag through RNA-Quast Blat to SL5 again to assign id's to the de novo contigs Count how many SL5 matches did we get? Should be 25K +. Run script to assign the soly IDs. Run Next FLow using these contigs and SL5 as the reference.
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              bbendick Brandon Bendickson added a comment -

              Reran Nag pipeline with success. RNA Spades, BLAT, and NEXTFLOW all complete without error. The new tsv files have the right sizes. For example, the salmon.merged.gene_counts.tsv now has 24,950 lines.

              Results are found in:
              /projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/start_fresh/Nag-run-3/results-3.14.0/star_salmon

              Show
              bbendick Brandon Bendickson added a comment - Reran Nag pipeline with success. RNA Spades, BLAT, and NEXTFLOW all complete without error. The new tsv files have the right sizes. For example, the salmon.merged.gene_counts.tsv now has 24,950 lines. Results are found in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/start_fresh/Nag-run-3/results-3.14.0/star_salmon
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              bbendick Brandon Bendickson added a comment -

              Going to add soly Ids and merge with old nextflow results as per tickets 3878 and 3883

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              bbendick Brandon Bendickson added a comment - Going to add soly Ids and merge with old nextflow results as per tickets 3878 and 3883
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              robofjoy Robert Reid added a comment -

              wc -l salmon.merged.transcript_counts.tsv
              24950 salmon.merged.transcript_counts.tsv

              Looks great. This appears to have the problem resolved. Case close back to the pipeline we go!

              Show
              robofjoy Robert Reid added a comment - wc -l salmon.merged.transcript_counts.tsv 24950 salmon.merged.transcript_counts.tsv Looks great. This appears to have the problem resolved. Case close back to the pipeline we go!

                People

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