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  1. IGB
  2. IGBF-3590

Re-run nextflow Ravi 30-804059537 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 30-804059537. SRP487154

          Directory: /projects/tomato_genome/fnb/dataprocessing/SRP487154

          For SL4 and SL5.

          For this task, we need to confirm and sanity-check the Ravi 30-804059537 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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              Issue Links

              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 created issue -
                Mdavis4290 Molly Davis made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                Mdavis4290 Molly Davis made changes -
                Description Experiment name is 30-804059537. Still waiting for {color:#d04437}SRP number{color}.


                For SL4 and SL5.

                For this task, we need to confirm and sanity-check the Ravi 30-681594536 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.                 		Experiment name is 30-804059537. Still waiting for {color:#d04437}SRP number{color}.


                For SL4 and SL5.

                For this task, we need to confirm and sanity-check the Ravi 30-804059537 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.
                Mdavis4290 Molly Davis made changes -
                Link This issue relates to IGBF-3499 [ IGBF-3499 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 [ 186 ] Spring 2, Spring 3 [ 186, 187 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                Mdavis4290 Molly Davis made changes -
                Sprint Spring 2, Spring 3 [ 186, 187 ] Spring 2 [ 186 ]
                Mdavis4290 Molly Davis made changes -
                Description Experiment name is 30-804059537. Still waiting for {color:#d04437}SRP number{color}.


                For SL4 and SL5.

                For this task, we need to confirm and sanity-check the Ravi 30-804059537 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.                 		Experiment name is 30-804059537. SRP487154


                For SL4 and SL5.

                For this task, we need to confirm and sanity-check the Ravi 30-804059537 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.
                Mdavis4290 Molly Davis made changes -
                Sprint Spring 2 [ 186 ] Spring 2, Summer 1 [ 186, 195 ]
                Mdavis4290 Molly Davis made changes -
                Rank Ranked higher
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
                Permalink
                Mdavis4290 Molly Davis added a comment -

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

                Show
                Mdavis4290 Molly Davis added a comment - Used this document to run the pipeline : https://docs.google.com/document/d/1ig9ET-ykXF5nAX3P487cXWmZDGUlQpcwrvFXpbyP5vw/edit
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2, Summer 1 [ 186, 195 ] Spring 2, Summer 1, Summer 2 [ 186, 195, 196 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                Mdavis4290 Molly Davis made changes -
                Description Experiment name is 30-804059537. SRP487154


                For SL4 and SL5.

                For this task, we need to confirm and sanity-check the Ravi 30-804059537 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.                 		Experiment name is 30-804059537. SRP487154

                Directory: /projects/tomato_genome/fnb/dataprocessing/SRP487154


                For SL4 and SL5.

                For this task, we need to confirm and sanity-check the Ravi 30-804059537 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.
                Hide
                Permalink
                Mdavis4290 Molly Davis added a comment - - edited

                Branch: https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3590
                Re-run Directory SL4: /projects/tomato_genome/fnb/dataprocessing/SRP487154/nfcore-SL4/results/star_salmon
                Re-run Directory SL5: /projects/tomato_genome/fnb/dataprocessing/SRP487154/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 - - edited Branch : https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3590 Re-run Directory SL4 : /projects/tomato_genome/fnb/dataprocessing/SRP487154/nfcore-SL4/results/star_salmon Re-run Directory SL5 : /projects/tomato_genome/fnb/dataprocessing/SRP487154/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"
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Robert Reid [ robertreid ]
                Hide
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                Mdavis4290 Molly Davis added a comment -

                PR: https://bitbucket.org/hotpollen/pistil-rna-seq/pull-requests/16

                Show
                Mdavis4290 Molly Davis added a comment - PR: https://bitbucket.org/hotpollen/pistil-rna-seq/pull-requests/16
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2, Summer 1, Summer 2 [ 186, 195, 196 ] Spring 2, Summer 1, Summer 2, Summer 3 [ 186, 195, 196, 197 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                robofjoy Robert Reid made changes -
                Assignee Robert Reid [ robertreid ] Brandon Bendickson [ bbendick ]
                Hide
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                bbendick Brandon Bendickson added a comment -

                SL4

                All files have reasonable sizes
                Every "FJ.bed.gz" file (63 files) has a corresponding "FJ.bed.gz.tbi" index file (63 files)
                Every Bam file (63 files) has a corresponding "FJ.bed.gz" file and a corresponding "scaled.bedgraph.gz" file (63 files).
                Every scaled.bedgraph.gz has a corresponding scaled.bedgraph.gz.tbi (63 files)

                Seems everything is correct!

                Show
                bbendick Brandon Bendickson added a comment - SL4 All files have reasonable sizes Every "FJ.bed.gz" file (63 files) has a corresponding "FJ.bed.gz.tbi" index file (63 files) Every Bam file (63 files) has a corresponding "FJ.bed.gz" file and a corresponding "scaled.bedgraph.gz" file (63 files). Every scaled.bedgraph.gz has a corresponding scaled.bedgraph.gz.tbi (63 files) Seems everything is correct!
                Hide
                Permalink
                bbendick Brandon Bendickson added a comment -

                SL5

                All files have reasonable sizes (only files with zero size are the .err files)
                Every "FJ.bed.gz" file (63) has a corresponding "FJ.bed.gz.tbi" (63) index file
                Every bam file (63) has a corresponding "FJ.bed.gz" file
                Every bam file has a corresponding "scaled.bedgraph.gz" file (63)
                Every "scaled.bedgraph.gz" has a corresponding "scaled.bedgraph.gz.tbi" (63)

                Everything seems correct!

                Show
                bbendick Brandon Bendickson added a comment - SL5 All files have reasonable sizes (only files with zero size are the .err files) Every "FJ.bed.gz" file (63) has a corresponding "FJ.bed.gz.tbi" (63) index file Every bam file (63) has a corresponding "FJ.bed.gz" file Every bam file has a corresponding "scaled.bedgraph.gz" file (63) Every "scaled.bedgraph.gz" has a corresponding "scaled.bedgraph.gz.tbi" (63) Everything seems correct!
                robofjoy Robert Reid made changes -
                Assignee Brandon Bendickson [ bbendick ] Robert Reid [ robertreid ]
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                robofjoy Robert Reid added a comment -

                Great, this is what we are looking to confirm.

                Show
                robofjoy Robert Reid added a comment - Great, this is what we are looking to confirm.
                robofjoy Robert Reid made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                robofjoy Robert Reid made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                robofjoy Robert Reid made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                robofjoy Robert Reid made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                robofjoy Robert Reid made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                robofjoy Robert Reid made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                robofjoy Robert Reid made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

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

                    Dates

                    • Created:
                      Updated:
                      Resolved: