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  1. IGB
  2. IGBF-3589

Re-run nextflow Ravi 30-681594536 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:
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          Description

          Experiment name is 30-681594536. SRP486761

          Directory: /projects/tomato_genome/fnb/dataprocessing/SRP486761

          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.

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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

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                Mdavis4290 Molly Davis added a comment -

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

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

                Branch: https://bitbucket.org/mdavis4290/molly-pistil-rna-seq/branch/IGBF-3589
                Re-run Directory SL4: /projects/tomato_genome/fnb/dataprocessing/SRP486761/nfcore-SL4/results/star_salmon
                Re-run Directory SL5: /projects/tomato_genome/fnb/dataprocessing/SRP486761/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-3589 Re-run Directory SL4: /projects/tomato_genome/fnb/dataprocessing/SRP486761/nfcore-SL4/results/star_salmon Re-run Directory SL5: /projects/tomato_genome/fnb/dataprocessing/SRP486761/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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                robofjoy Robert Reid added a comment -

                Both SL4 and SL5 folders have the same 235 files.

                SL4
                55 bam files and bai files for each. Sizes look correct.
                55 bedgraphs that are 120MB in size.
                55 gzipped bed files that are 7 MB in size.
                The tbi files seem to match the same 55 in number and all are small kb in size.

                Sl5
                55 bam files and bai files for each. Sizes look correct.
                55 bedgraphs that are 120MB in size.
                55 gzipped bed files that are 7 MB in size.
                The tbi files seem to match the same 55 in number and all are small kb in size.
                A few bedgraphs look smaller:
                rw-rr- 1 mdavi258 tomato_genome 80M Jun 6 10:34 SRR27782293.scaled.bedgraph.gz
                rw-rr- 1 mdavi258 tomato_genome 81M Jun 6 10:35 SRR27782329.scaled.bedgraph.gz
                rw-rr- 1 mdavi258 tomato_genome 94M Jun 6 10:36 SRR27782312.scaled.bedgraph.gz
                rw-rr- 1 mdavi258 tomato_genome 103M Jun 6 10:36 SRR27782326.scaled.bedgraph.gz
                rw-rr- 1 mdavi258 tomato_genome 113M Jun 6 10:37 SRR27782325.scaled.bedgraph.gz
                rw-rr- 1 mdavi258 tomato_genome 110M Jun 6 10:37 SRR27782311.scaled.bedgraph.gz
                rw-rr- 1 mdavi258 tomato_genome 82M Jun 6 10:37 SRR27782294.scaled.bedgraph.gz

                But that is most likely still within range of the others.
                All looks good to proceed!

                Show
                robofjoy Robert Reid added a comment - Both SL4 and SL5 folders have the same 235 files. SL4 55 bam files and bai files for each. Sizes look correct. 55 bedgraphs that are 120MB in size. 55 gzipped bed files that are 7 MB in size. The tbi files seem to match the same 55 in number and all are small kb in size. Sl5 55 bam files and bai files for each. Sizes look correct. 55 bedgraphs that are 120MB in size. 55 gzipped bed files that are 7 MB in size. The tbi files seem to match the same 55 in number and all are small kb in size. A few bedgraphs look smaller: rw-r r - 1 mdavi258 tomato_genome 80M Jun 6 10:34 SRR27782293.scaled.bedgraph.gz rw-r r - 1 mdavi258 tomato_genome 81M Jun 6 10:35 SRR27782329.scaled.bedgraph.gz rw-r r - 1 mdavi258 tomato_genome 94M Jun 6 10:36 SRR27782312.scaled.bedgraph.gz rw-r r - 1 mdavi258 tomato_genome 103M Jun 6 10:36 SRR27782326.scaled.bedgraph.gz rw-r r - 1 mdavi258 tomato_genome 113M Jun 6 10:37 SRR27782325.scaled.bedgraph.gz rw-r r - 1 mdavi258 tomato_genome 110M Jun 6 10:37 SRR27782311.scaled.bedgraph.gz rw-r r - 1 mdavi258 tomato_genome 82M Jun 6 10:37 SRR27782294.scaled.bedgraph.gz But that is most likely still within range of the others. All looks good to proceed!
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                Mdavis4290 Molly Davis added a comment -

                PR: https://bitbucket.org/hotpollen/pistil-rna-seq/pull-requests/14

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                Mdavis4290 Molly Davis added a comment - PR : https://bitbucket.org/hotpollen/pistil-rna-seq/pull-requests/14
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                ann.loraine Ann Loraine added a comment -

                PR is merged. Thank you Robert Reid for making note of the unusual file sizes.
                Need to compare multiqc reports pre- and post-SRA submission to sanity-check that the data deposition succeeded, using the resources created here.
                Moving to DONE.

                Show
                ann.loraine Ann Loraine added a comment - PR is merged. Thank you Robert Reid for making note of the unusual file sizes. Need to compare multiqc reports pre- and post-SRA submission to sanity-check that the data deposition succeeded, using the resources created here. Moving to DONE.

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    Mdavis4290 Molly Davis
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                      Updated:
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