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  1. IGB
  2. IGBF-3735

Run the latest version of the nf-core/rnaseq pipeline with tardigrade data

        Details

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

          Description

          Task: Continue the workflow started in IGBF-3708 by running the latest version of the nf-core/rnaseq pipeline with the downloaded fastq files. Continue to document the commands used to run this pipeline (see IGBF-3721).

          For reference, here is that workflow once again:

          1. Run prefetch.sh to get .sra files for the list of SRR accessions.
          2. Check that the .sra files got downloaded correctly.
          3. Run fasterq-dump to make fastq files from the .sra files.
          4. Compress the fastq files with gzip using gzip.sh and submit to slurm queue using sbatch-doIt.sh
          5. Run nf-core/rnaseq pipeline latest version. For this, you have to make a "parameter" file and provide gene annotations (.gtf file), genome annotations (.bed file), and genome assembly (.fasta file).
          6. Check that the pipeline ran correctly.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3790 Run nf-core/rnaseq v 3.14 on SRP484252 (2024 Goldstein Lab)

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3708 Download tardigrade RNA-Seq data onto cluster

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3721 Document Tardigrade RNA-Seq Pipeline

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine added a comment - - edited

                This is now done. AL ran the latest, most accurate version of the pipeline as part of a linked ticket IGBF-3790, and described the experience.

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                ann.loraine Ann Loraine added a comment - - edited This is now done. AL ran the latest, most accurate version of the pipeline as part of a linked ticket IGBF-3790 , and described the experience.

                  People

                  • Assignee:
                    pkulzer Paige Kulzer
                    Reporter:
                    pkulzer Paige Kulzer
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                    Dates

                    • Created:
                      Updated:
                      Resolved: