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  1. IGB
  2. IGBF-3144

Make annots.xml for RNA-Seq junction, alignment, and coverage graphs

        Details

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

          Description

          This is needed to deploy the new data files for visualization in IGB.

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              is blocked by

              Task - A task that needs to be done. IGBF-3040 Create samplesheet with SRR run identifiers and experimental attributes

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3143 Run RNA-Seq data processing pipeline on positive splicing control and experimental samples

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3162 Generate scaled coverage graphs for RNA-Seq alignments

              • Major - Major loss of function.
              • Closed
              relates to

              Task - A task that needs to be done. IGBF-3230 Visualize alternative splicing events

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine added a comment -

                To review that the data files were made correctly, we need to look at them in IGB. So, for this, I need to create the annots.xml files and add them to a Quickload site.

                Show
                ann.loraine Ann Loraine added a comment - To review that the data files were made correctly, we need to look at them in IGB. So, for this, I need to create the annots.xml files and add them to a Quickload site.
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                ann.loraine Ann Loraine added a comment -

                Copied annots.xml generating code from flavonoid-rnaseq/src to splicing-analysis/src. Need to update the code with new sample names.

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                ann.loraine Ann Loraine added a comment - Copied annots.xml generating code from flavonoid-rnaseq/src to splicing-analysis/src. Need to update the code with new sample names.
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                ann.loraine Ann Loraine added a comment - - edited

                Copying data to renci host. Started a tmux sessions and then did:

                [aloraine@str-i1 star_salmon]$ pwd
/nobackup/tomato_genome/alt_splicing/SRP252265/results/star_salmon
[aloraine@str-i1 star_salmon]$ scp -o 'ProxyJump aloraine@hop.renci.org' *.bam.bai aloraine@lorainelab-quickload.scidas.org:/projects/igbquickload/lorainelab/www/main/htdocs/hotpollen/S_lycopersicum_Jun_2022/data/.
[aloraine@str-i1 star_salmon]$ scp -o 'ProxyJump aloraine@hop.renci.org' *.bam aloraine@lorainelab-quickload.scidas.org:/projects/igbquickload/lorainelab/www/main/htdocs/hotpollen/S_lycopersicum_Jun_2022/data/.
                Show
                ann.loraine Ann Loraine added a comment - - edited Copying data to renci host. Started a tmux sessions and then did: [aloraine@str-i1 star_salmon]$ pwd /nobackup/tomato_genome/alt_splicing/SRP252265/results/star_salmon [aloraine@str-i1 star_salmon]$ scp -o 'ProxyJump aloraine@hop.renci.org' *.bam.bai aloraine@lorainelab-quickload.scidas.org:/projects/igbquickload/lorainelab/www/main/htdocs/hotpollen/S_lycopersicum_Jun_2022/data/. [aloraine@str-i1 star_salmon]$ scp -o 'ProxyJump aloraine@hop.renci.org' *.bam aloraine@lorainelab-quickload.scidas.org:/projects/igbquickload/lorainelab/www/main/htdocs/hotpollen/S_lycopersicum_Jun_2022/data/.
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                ann.loraine Ann Loraine added a comment -

                Working on branch https://bitbucket.org/aloraine/splicing-analysis/branch/IGBF-3144

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                ann.loraine Ann Loraine added a comment - Working on branch https://bitbucket.org/aloraine/splicing-analysis/branch/IGBF-3144
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                ann.loraine Ann Loraine added a comment -

                makeAnnotsXml.py creates quickload directory structure with meta-data files, including annots.xml.
                However, the display folder structure has a bug - only one subfolder named is made.

                Show
                ann.loraine Ann Loraine added a comment - makeAnnotsXml.py creates quickload directory structure with meta-data files, including annots.xml. However, the display folder structure has a bug - only one subfolder named is made.
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                ann.loraine Ann Loraine added a comment -

                Fixed above bug.
                Quickload site is written to subdirectory "quickload" inside ManageQuickload folder. Using fully qualified file name in file tags. Files are deployed to renci host http://lorainelab-quickload.scidas.org/hotpollen/S_lycopersicum_Jun_2022/[ srp accession number ]/[ file name]

                Checked that could load a few files in IGB. Made some png files on first chromosome.

                Show
                ann.loraine Ann Loraine added a comment - Fixed above bug. Quickload site is written to subdirectory "quickload" inside ManageQuickload folder. Using fully qualified file name in file tags. Files are deployed to renci host http://lorainelab-quickload.scidas.org/hotpollen/S_lycopersicum_Jun_2022/[ srp accession number ]/[ file name] Checked that could load a few files in IGB. Made some png files on first chromosome.

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: