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  1. IGB
  2. IGBF-3244

Run rnaseq pipeline on mark-2022-timeseries

        Details

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

          Description

          Run nextflow for the dataset in:

          /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

          This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

          Kindly run the nf-core pipeline in this location:

          • /nobackup/tomato_genome/mark-2022-timeseries

          Note on attached files:

          • multiqc report on the entire run done by Rasha is attached, copied from google drive location GTTR-NSF PGRP - 2020-24 IOS-1939255 > Experiments > Rasha_RNA-seq_Time_Course > Results > multiqc > star_salmon > multiqc_report.html
          • Link: https://drive.google.com/drive/u/1/folders/1GJnZefP-7TE-ch-c0lblGZMOqpwSgZRK
          • 2023-01-18_timeseries_multiqc_report.html - MultiQC report from re-running nextflow (Molly's new work)\
          • sample.csv - new samples file used to re-run nextflow (Molly's new work)

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3246 Generate list of EBSeq-HMM clusters for varieties and conditions

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3245 Investigate: Why do coverage graphs look different?

              • Major - Major loss of function.
              • To-Do

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Summary Re-run nfcore rnaseq pipeline for seedlingPollen data Run nfcore rnaseq pipeline for time course data
                ann.loraine Ann Loraine made changes -
                Description We need to re-run nf-core pipeline with a new strandedness parameter as noted in attached multiqc report.
                ann.loraine Ann Loraine made changes -
                Description Run nextflow for the dataset in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

                Run the nf-core pipeline in this location: /

                * nobackup/tomato_genome/mark-2022-timeseries
                ann.loraine Ann Loraine made changes -
                Summary Run nfcore rnaseq pipeline for time course data Run rnaseq pipeline on
                ann.loraine Ann Loraine made changes -
                Summary Run rnaseq pipeline on Run rnaseq pipeline on mark-2022-timeseries
                ann.loraine Ann Loraine made changes -
                Attachment 2022-11-24_multiqc_report.html [ 17651 ]
                ann.loraine Ann Loraine made changes -
                Description Run nextflow for the dataset in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

                Run the nf-core pipeline in this location: /

                * nobackup/tomato_genome/mark-2022-timeseries                 		Run nextflow for the dataset in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

                Run the nf-core pipeline in this location: /

                * nobackup/tomato_genome/mark-2022-timeseries

                Note on attachments:

                * multiqc report on the entire run done by Rasha is attached, copied from google drive location GTTR-NSF PGRP - 2020-24 IOS-1939255 > Experiments > Rasha_RNA-seq_Time_Course > Results > multiqc > star_salmon > multiqc_report.html
                ann.loraine Ann Loraine made changes -
                Description Run nextflow for the dataset in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

                Run the nf-core pipeline in this location: /

                * nobackup/tomato_genome/mark-2022-timeseries

                Note on attachments:

                * multiqc report on the entire run done by Rasha is attached, copied from google drive location GTTR-NSF PGRP - 2020-24 IOS-1939255 > Experiments > Rasha_RNA-seq_Time_Course > Results > multiqc > star_salmon > multiqc_report.html                 		Run nextflow for the dataset in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

                Kindly run the nf-core pipeline in this location: /

                * nobackup/tomato_genome/mark-2022-timeseries

                Note on attached files:

                * multiqc report on the entire run done by Rasha is attached, copied from google drive location GTTR-NSF PGRP - 2020-24 IOS-1939255 > Experiments > Rasha_RNA-seq_Time_Course > Results > multiqc > star_salmon > multiqc_report.html
                ann.loraine Ann Loraine made changes -
                Description Run nextflow for the dataset in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

                Kindly run the nf-core pipeline in this location: /

                * nobackup/tomato_genome/mark-2022-timeseries

                Note on attached files:

                * multiqc report on the entire run done by Rasha is attached, copied from google drive location GTTR-NSF PGRP - 2020-24 IOS-1939255 > Experiments > Rasha_RNA-seq_Time_Course > Results > multiqc > star_salmon > multiqc_report.html                 		Run nextflow for the dataset in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

                Kindly run the nf-core pipeline in this location:

                * /nobackup/tomato_genome/mark-2022-timeseries

                Note on attached files:

                * multiqc report on the entire run done by Rasha is attached, copied from google drive location GTTR-NSF PGRP - 2020-24 IOS-1939255 > Experiments > Rasha_RNA-seq_Time_Course > Results > multiqc > star_salmon > multiqc_report.html
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Description Run nextflow for the dataset in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

                Kindly run the nf-core pipeline in this location:

                * /nobackup/tomato_genome/mark-2022-timeseries

                Note on attached files:

                * multiqc report on the entire run done by Rasha is attached, copied from google drive location GTTR-NSF PGRP - 2020-24 IOS-1939255 > Experiments > Rasha_RNA-seq_Time_Course > Results > multiqc > star_salmon > multiqc_report.html                 		Run nextflow for the dataset in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

                Kindly run the nf-core pipeline in this location:

                * /nobackup/tomato_genome/mark-2022-timeseries

                Note on attached files:

                * multiqc report on the entire run done by Rasha is attached, copied from google drive location GTTR-NSF PGRP - 2020-24 IOS-1939255 > Experiments > Rasha_RNA-seq_Time_Course > Results > multiqc > star_salmon > multiqc_report.html
                * Link: https://drive.google.com/drive/u/1/folders/1GJnZefP-7TE-ch-c0lblGZMOqpwSgZRK
                Hide
                Permalink
                Mdavis4290 Molly Davis added a comment - - edited

                Next steps: Find or make a csv sample sheet and change strandedness to 'reverse' to run nextflow.
                sample.csv

                Show
                Mdavis4290 Molly Davis added a comment - - edited Next steps: Find or make a csv sample sheet and change strandedness to 'reverse' to run nextflow. sample.csv
                Mdavis4290 Molly Davis made changes -
                Attachment sample.csv [ 17652 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Attachment Screen Shot 2023-01-18 at 4.45.24 PM.png [ 17654 ]
                Hide
                Permalink
                Mdavis4290 Molly Davis added a comment - - edited


                Nextflow Pipeline Ran Successfully!
                Directory: /nobackup/tomato_genome/mark-2022-timeseries
                Next steps: Rename sorted bam files and make scaled coverage graphs.

                Show
                Mdavis4290 Molly Davis added a comment - - edited Nextflow Pipeline Ran Successfully! Directory: /nobackup/tomato_genome/mark-2022-timeseries Next steps: Rename sorted bam files and make scaled coverage graphs.
                Hide
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                Mdavis4290 Molly Davis added a comment - - edited

                Scaled coverage graphs have been made and are located: 

                /nobackup/tomato_genome/mark-2022-timeseries/results/star_salmon

                Notes: I can move the coverage graphs to their own directory if you would like. Let me know!

                Multiqc report: 

                scp mdavi258@hpc.uncc.edu:/nobackup/tomato_genome/mark-2022-timeseries/results/multiqc/star_salmon/multiqc_report.html timeseries_multiqc_report.html

                [^timeseries_multiqc_report.html]

                Notes: Multiqc report seems to show better mapping and correct strandedness now compared to the previous report and nextflow run.

                Next step: Pipeline, coverage graphs, and Multiqc report need to be reviewed.
                [~aloraine]

                Show
                Mdavis4290 Molly Davis added a comment - - edited Scaled coverage graphs have been made and are located: /nobackup/tomato_genome/mark-2022-timeseries/results/star_salmon Notes: I can move the coverage graphs to their own directory if you would like. Let me know! Multiqc report: scp mdavi258@hpc.uncc.edu:/nobackup/tomato_genome/mark-2022-timeseries/results/multiqc/star_salmon/multiqc_report.html timeseries_multiqc_report.html [^timeseries_multiqc_report.html] Notes: Multiqc report seems to show better mapping and correct strandedness now compared to the previous report and nextflow run. Next step : Pipeline, coverage graphs, and Multiqc report need to be reviewed. [~aloraine]
                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 -
                Attachment timeseries_multiqc_report.html [ 17658 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                I reviewed multiqc report and noticed no problems.
                I migrated coverage graphs and bam files to igb quickload host and updated makeAnnotsXml.py in https://bitbucket.org/hotpollen/splicing-analysis/src/main/ to use the new files.
                See: ManageQuickload/makeAnnotsXml.py and ManageQuickload/quickload/S_lycopersicum_Jun_2022/annots.xml.

                Moving to DONE.

                Show
                ann.loraine Ann Loraine added a comment - I reviewed multiqc report and noticed no problems. I migrated coverage graphs and bam files to igb quickload host and updated makeAnnotsXml.py in https://bitbucket.org/hotpollen/splicing-analysis/src/main/ to use the new files. See: ManageQuickload/makeAnnotsXml.py and ManageQuickload/quickload/S_lycopersicum_Jun_2022/annots.xml. Moving to DONE.
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ] Molly Davis [ molly ]
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment - - edited

                I noticed that coverage graphs for this new dataset, which is strand-specific and paired-end, look a bit different, with different patterns of peaks and valleys, compared to earlier data from Genewiz where the data were paired-end and NOT strand-specific. Weird. I don't know why this occurred.

                For example, see:

                GenomeBrowserImages/TimeCourseVsOlderData-CoverageGraphProfileDifference.png

                Creating new ticket to investigate.

                Show
                ann.loraine Ann Loraine added a comment - - edited I noticed that coverage graphs for this new dataset, which is strand-specific and paired-end, look a bit different, with different patterns of peaks and valleys, compared to earlier data from Genewiz where the data were paired-end and NOT strand-specific. Weird. I don't know why this occurred. For example, see: GenomeBrowserImages/TimeCourseVsOlderData-CoverageGraphProfileDifference.png Creating new ticket to investigate.
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3245 [ IGBF-3245 ]
                ann.loraine Ann Loraine made changes -
                Attachment timeseries_multiqc_report.html [ 17658 ]
                ann.loraine Ann Loraine made changes -
                Attachment 2023-01-18_timeseries_multiqc_report.html [ 17667 ]
                ann.loraine Ann Loraine made changes -
                Description Run nextflow for the dataset in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

                Kindly run the nf-core pipeline in this location:

                * /nobackup/tomato_genome/mark-2022-timeseries

                Note on attached files:

                * multiqc report on the entire run done by Rasha is attached, copied from google drive location GTTR-NSF PGRP - 2020-24 IOS-1939255 > Experiments > Rasha_RNA-seq_Time_Course > Results > multiqc > star_salmon > multiqc_report.html
                * Link: https://drive.google.com/drive/u/1/folders/1GJnZefP-7TE-ch-c0lblGZMOqpwSgZRK                 		Run nextflow for the dataset in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

                Kindly run the nf-core pipeline in this location:

                * /nobackup/tomato_genome/mark-2022-timeseries

                Note on attached files:

                * multiqc report on the entire run done by Rasha is attached, copied from google drive location GTTR-NSF PGRP - 2020-24 IOS-1939255 > Experiments > Rasha_RNA-seq_Time_Course > Results > multiqc > star_salmon > multiqc_report.html
                * Link: https://drive.google.com/drive/u/1/folders/1GJnZefP-7TE-ch-c0lblGZMOqpwSgZRK
                * 2023-01-18_timeseries_multiqc_report.html - MultiQC report from re-running nextflow (Molly's new work)
                ann.loraine Ann Loraine made changes -
                Description Run nextflow for the dataset in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

                Kindly run the nf-core pipeline in this location:

                * /nobackup/tomato_genome/mark-2022-timeseries

                Note on attached files:

                * multiqc report on the entire run done by Rasha is attached, copied from google drive location GTTR-NSF PGRP - 2020-24 IOS-1939255 > Experiments > Rasha_RNA-seq_Time_Course > Results > multiqc > star_salmon > multiqc_report.html
                * Link: https://drive.google.com/drive/u/1/folders/1GJnZefP-7TE-ch-c0lblGZMOqpwSgZRK
                * 2023-01-18_timeseries_multiqc_report.html - MultiQC report from re-running nextflow (Molly's new work)                 		Run nextflow for the dataset in:

                /projects/tomato_genome/rnaseq/mark-2022-timeseries/30-771363348/00_fastq

                This is the "time course" dataset discussed by Rasha at the 2023-01-17 group meeting. Note that she has already run nextflow for this dataset but using "unstranded" for the "strandedness" parameter in the "samples.csv" file. It turns out this dataset comes from libraries that were created using a strand-specific RNA-Seq library. To be on the safe side, we should re-run the pipeline using parameter "reverse", as indicated in the multiQC report included with Rasha's initial run of the nextflow nf-core rnaseq pipeline.

                Kindly run the nf-core pipeline in this location:

                * /nobackup/tomato_genome/mark-2022-timeseries

                Note on attached files:

                * multiqc report on the entire run done by Rasha is attached, copied from google drive location GTTR-NSF PGRP - 2020-24 IOS-1939255 > Experiments > Rasha_RNA-seq_Time_Course > Results > multiqc > star_salmon > multiqc_report.html
                * Link: https://drive.google.com/drive/u/1/folders/1GJnZefP-7TE-ch-c0lblGZMOqpwSgZRK
                * 2023-01-18_timeseries_multiqc_report.html - MultiQC report from re-running nextflow (Molly's new work)\
                * sample.csv - new samples file used to re-run nextflow (Molly's new work)
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3246 [ IGBF-3246 ]

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: