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  1. IGB
  2. IGBF-3450

Run nf-core/rnaseq pipeline using SL4 target genome assembly

        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:

          Create BAM, coverage graph, and junction files for the Muday Lab time course data using SL4 genome and gene annotations as the target for alignment.

          When complete, please note the location of files created.

          Note: Don't use the renamed files. Use the original input files prior to their being renamed.

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              9 older comments
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              Mdavis4290 Molly Davis added a comment - - edited

              chmod g+w /projects/tomato_genome/fnb/dataprocessing/muday-144/nfcore-SL4/results
              chmod -R g+w *

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              Mdavis4290 Molly Davis added a comment - - edited chmod g+w /projects/tomato_genome/fnb/dataprocessing/muday-144/nfcore-SL4/results chmod -R g+w *
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              ann.loraine Ann Loraine added a comment -

              Moved or copied nf-core output files to HPC file system location: /projects/tomato_genome/fnb/dataprocessing/muday-144/for_quickload/S_lycopersicum_Sep_2019/muday-2022-timeseries

              On data.bioviz.org host, launched "screen" session and commenced copying nf-core output files to data.bioviz.org with:

              cd /mnt/igbdata/hotpollen/S_lycopersicum_Sep_2019
rsync -rz aloraine@10.16.115.244:/projects/tomato_genome/fnb/dataprocessing/muday-144/for_quickload/S_lycopersicum_Sep_2019/muday-2022-timeseries .
              Show
              ann.loraine Ann Loraine added a comment - Moved or copied nf-core output files to HPC file system location: /projects/tomato_genome/fnb/dataprocessing/muday-144/for_quickload/S_lycopersicum_Sep_2019/muday-2022-timeseries On data.bioviz.org host, launched "screen" session and commenced copying nf-core output files to data.bioviz.org with: cd /mnt/igbdata/hotpollen/S_lycopersicum_Sep_2019 rsync -rz aloraine@10.16.115.244:/projects/tomato_genome/fnb/dataprocessing/muday-144/for_quickload/S_lycopersicum_Sep_2019/muday-2022-timeseries .
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              ann.loraine Ann Loraine added a comment -

              Added new SL4 data to the annots.xml configuration files for visualization in IGB. Updated "main" branch of https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/

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              ann.loraine Ann Loraine added a comment - Added new SL4 data to the annots.xml configuration files for visualization in IGB. Updated "main" branch of https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/
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              ann.loraine Ann Loraine added a comment -

              Review passes:

              • counts file is added to the repo
              • data files are added to data.bioviz.org for visualization and permissions set to allow delivery via the Web server
              • also added multiqc report and its input data to the data.bioviz.org deployment site for easier visualization

              Note that these data are NOT using renamed labels. The files that were processed match the original file names from the sequencer.

              Moving to ready for testing.

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              ann.loraine Ann Loraine added a comment - Review passes: counts file is added to the repo data files are added to data.bioviz.org for visualization and permissions set to allow delivery via the Web server also added multiqc report and its input data to the data.bioviz.org deployment site for easier visualization Note that these data are NOT using renamed labels. The files that were processed match the original file names from the sequencer. Moving to ready for testing.
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              Mdavis4290 Molly Davis added a comment - - edited

              Testing:

              Moving to done!

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              Mdavis4290 Molly Davis added a comment - - edited Testing : Count file is present in repo: 72_F3H_PollenTube/muday-144-SL4_salmon.merged.gene_counts.tsv SL5 (PT time GM lab) and SL4 (PT time GM lab) datasets for Muday-144 are present and accessible in IGB quickload Found report and input data on deployment site here: https://data.bioviz.org/hotpollen/S_lycopersicum_Sep_2019/muday-2022-timeseries/ Moving to done!

                People

                • Assignee:
                  Mdavis4290 Molly Davis
                  Reporter:
                  ann.loraine Ann Loraine
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                  • Created:
                    Updated:
                    Resolved: