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  1. IGB
  2. IGBF-3591

Re-run nextflow Ravi 30-605730043 data for SL4 and SL5 with data dowloaded from SRA

        Details

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

          Description

          Experiment name is 30-605730043. SRP482647

          Directory: /projects/tomato_genome/fnb/dataprocessing/SRP482647

          For SL4 and SL5.

          For this task, we need to confirm and sanity-check the Ravi 30-605730043 data that Rob uploaded and submitted to the Sequence Read Archive.
          If the data are good, we will replace all the existing BAM, junctions, etc. files deployed in the "hotpollen" quickload site with newly processed data.
          For this task:

          • Check SRP on NCBI and review submission
          • Download the data onto the cluster by using the SRP name
          • Run nf-core/rnaseq pipeline
          • Run our coverage graph and junctions scripts on the data

          Note that all files should now use their "SRR" names instead of the existing file names.

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              relates to

              Task - A task that needs to be done. IGBF-3499 Complete evaluation of RNA-Seq dataset submissions

              • Major - Major loss of function.
              • Closed

                Activity

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                Mdavis4290 Molly Davis added a comment -

                Used this document to run Pipeline: https://docs.google.com/document/d/1ig9ET-ykXF5nAX3P487cXWmZDGUlQpcwrvFXpbyP5vw/edit

                Show
                Mdavis4290 Molly Davis added a comment - Used this document to run Pipeline : https://docs.google.com/document/d/1ig9ET-ykXF5nAX3P487cXWmZDGUlQpcwrvFXpbyP5vw/edit
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                Mdavis4290 Molly Davis added a comment -

                Branch: https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3591
                Re-run Directory SL4: /projects/tomato_genome/fnb/dataprocessing/SRP482647/nfcore-SL4/results/star_salmon
                Re-run Directory SL5: /projects/tomato_genome/fnb/dataprocessing/SRP482647/nfcore-SL5/results/star_salmon
                Reviewer:
                Check that files have reasonable sizes (no "zero" size files, for example)
                Check that every "FJ.bed.gz" file has a corresponding "FJ.bed.gz.tbi" index file
                Check that every bam file has a corresponding "FJ.bed.gz" file
                Check that every bam file has a corresponding "scaled.bedgraph.gz" file
                Check that every "scaled.bedgraph.gz" has a corresponding "scaled.bedgraph.gz.tbi"

                Show
                Mdavis4290 Molly Davis added a comment - Branch : https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3591 Re-run Directory SL4 : /projects/tomato_genome/fnb/dataprocessing/SRP482647/nfcore-SL4/results/star_salmon Re-run Directory SL5 : /projects/tomato_genome/fnb/dataprocessing/SRP482647/nfcore-SL5/results/star_salmon Reviewer : Check that files have reasonable sizes (no "zero" size files, for example) Check that every "FJ.bed.gz" file has a corresponding "FJ.bed.gz.tbi" index file Check that every bam file has a corresponding "FJ.bed.gz" file Check that every bam file has a corresponding "scaled.bedgraph.gz" file Check that every "scaled.bedgraph.gz" has a corresponding "scaled.bedgraph.gz.tbi"
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                Mdavis4290 Molly Davis added a comment -

                PR: https://bitbucket.org/hotpollen/pistil-rna-seq/pull-requests/15

                Show
                Mdavis4290 Molly Davis added a comment - PR: https://bitbucket.org/hotpollen/pistil-rna-seq/pull-requests/15
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                robofjoy Robert Reid added a comment -

                I will walk Brandon through how to check out the files for file integrity. (Rob)

                This will enable him to be a reviewer for tasks like this.
                R

                Show
                robofjoy Robert Reid added a comment - I will walk Brandon through how to check out the files for file integrity. (Rob) This will enable him to be a reviewer for tasks like this. R
                Hide
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                bbendick Brandon Bendickson added a comment -

                SL4

                All files have reasonable sizes, the only files with zero size are the .err files.
                Every "FJ.bed.gz" file (10) has a corresponding "FJ.bed.gz.tbi" index file (10)
                Every bam file (10) has a corresponding "FJ.bed.gz" file
                Every bam file has a corresponding "scaled.bedgraph.gz" file (10)
                Every "scaled.bedgraph.gz" has a corresponding "scaled.bedgraph.gz.tbi" (10)

                Seems like everything is correct!

                Show
                bbendick Brandon Bendickson added a comment - SL4 All files have reasonable sizes, the only files with zero size are the .err files. Every "FJ.bed.gz" file (10) has a corresponding "FJ.bed.gz.tbi" index file (10) Every bam file (10) has a corresponding "FJ.bed.gz" file Every bam file has a corresponding "scaled.bedgraph.gz" file (10) Every "scaled.bedgraph.gz" has a corresponding "scaled.bedgraph.gz.tbi" (10) Seems like everything is correct!
                Hide
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                bbendick Brandon Bendickson added a comment -

                SL5

                All files have reasonable sizes, the only files with zero size are the .err files.
                Every "FJ.bed.gz" file (10) has a corresponding "FJ.bed.gz.tbi" index file (10)
                Every bam file (10) has a corresponding "FJ.bed.gz" file
                Every bam file has a corresponding "scaled.bedgraph.gz" file (10)
                Every "scaled.bedgraph.gz" has a corresponding "scaled.bedgraph.gz.tbi" (10)

                Seems like everything is correct

                Show
                bbendick Brandon Bendickson added a comment - SL5 All files have reasonable sizes, the only files with zero size are the .err files. Every "FJ.bed.gz" file (10) has a corresponding "FJ.bed.gz.tbi" index file (10) Every bam file (10) has a corresponding "FJ.bed.gz" file Every bam file has a corresponding "scaled.bedgraph.gz" file (10) Every "scaled.bedgraph.gz" has a corresponding "scaled.bedgraph.gz.tbi" (10) Seems like everything is correct
                Hide
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                robofjoy Robert Reid added a comment -

                Great, let's close the ticket!

                Show
                robofjoy Robert Reid added a comment - Great, let's close the ticket!

                  People

                  • Assignee:
                    robofjoy Robert Reid
                    Reporter:
                    Mdavis4290 Molly Davis
                  • Votes:
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                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: