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  1. IGB
  2. IGBF-2947

Investigate using nf-core/rnaseq pipeline

        Details

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

          Description

          Nextflow provides a standard type of RNA-Seq data pipeline called "nf-core/rnaseq" that we can potentially use for processing data in the Pollen PGRP and other related projects.

          For example, the following command shows an example of running this pipeline on a "single end" data set, using a reference genome indicated by the "--fasta" option:

          nextflow run nf-core/rnaseq -profile conda --singleEnd --reverseStranded --skipTrimming --reads '*.fastq.gz' --fasta 'ftp://ftp.ensembl.org/pub/release-99/fasta/rattus_norvegicus/dna_index/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz' --gtf 'ftp://ftp.ensembl.org/pub/release-99/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.99.gtf.gz' --fc_count_type transcript

          One major benefit of using this pipeline is that there is a lot of support for it in the larger bioinformatics community. There's a company (Sequera) that is supporting this and other Nextflow related projects.

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              relates to

              Task - A task that needs to be done. IGBF-2970 Re-run nf-core/rnaseq using proper strand designation and better sample prefix

              • 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

                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-2323 [ 18477 ]
                ann.loraine Ann Loraine made changes -
                Description
                {code}
                nextflow run nf-core/rnaseq -profile conda --singleEnd --reverseStranded --skipTrimming --reads '*.fastq.gz' --fasta 'ftp://ftp.ensembl.org/pub/release-99/fasta/rattus_norvegicus/dna_index/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz' --gtf 'ftp://ftp.ensembl.org/pub/release-99/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.99.gtf.gz' --fc_count_type transcript
                {code}                 		Nextflow provides a standard type of RNA-Seq data pipeline called "nf-core/rnaseq" that we can potentially use for processing data in the Pollen PGRP and other related projects.

                For example, the following command shows ab example of running this pipeline on a "single end" data set, using a reference genome indicated by the "--fasta" option:

                {code}
                nextflow run nf-core/rnaseq -profile conda --singleEnd --reverseStranded --skipTrimming --reads '*.fastq.gz' --fasta 'ftp://ftp.ensembl.org/pub/release-99/fasta/rattus_norvegicus/dna_index/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz' --gtf 'ftp://ftp.ensembl.org/pub/release-99/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.99.gtf.gz' --fc_count_type transcript
                {code}

                One major benefit of using this pipeline is that there is a lot of support for it in the larger bioinformatics community. There's a company (Sequera) that is supporting this and other Nextflow related projects, and

                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 3 2021 Sep 13 - Sep 24 [ 129 ] Fall 3 2021 Sep 13 - Sep 24, Fall 4 2021 Sep 27 - Oct 8 [ 129, 130 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Attachment 2021-09-28-rnaseq_pipeline_stdout.txt [ 16786 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Description Nextflow provides a standard type of RNA-Seq data pipeline called "nf-core/rnaseq" that we can potentially use for processing data in the Pollen PGRP and other related projects.

                For example, the following command shows ab example of running this pipeline on a "single end" data set, using a reference genome indicated by the "--fasta" option:

                {code}
                nextflow run nf-core/rnaseq -profile conda --singleEnd --reverseStranded --skipTrimming --reads '*.fastq.gz' --fasta 'ftp://ftp.ensembl.org/pub/release-99/fasta/rattus_norvegicus/dna_index/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz' --gtf 'ftp://ftp.ensembl.org/pub/release-99/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.99.gtf.gz' --fc_count_type transcript
                {code}

                One major benefit of using this pipeline is that there is a lot of support for it in the larger bioinformatics community. There's a company (Sequera) that is supporting this and other Nextflow related projects, and

                		Nextflow provides a standard type of RNA-Seq data pipeline called "nf-core/rnaseq" that we can potentially use for processing data in the Pollen PGRP and other related projects.

                For example, the following command shows an example of running this pipeline on a "single end" data set, using a reference genome indicated by the "--fasta" option:

                {code}
                nextflow run nf-core/rnaseq -profile conda --singleEnd --reverseStranded --skipTrimming --reads '*.fastq.gz' --fasta 'ftp://ftp.ensembl.org/pub/release-99/fasta/rattus_norvegicus/dna_index/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz' --gtf 'ftp://ftp.ensembl.org/pub/release-99/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.99.gtf.gz' --fc_count_type transcript
                {code}

                One major benefit of using this pipeline is that there is a lot of support for it in the larger bioinformatics community. There's a company (Sequera) that is supporting this and other Nextflow related projects, and

                nfreese Nowlan Freese made changes -
                Description Nextflow provides a standard type of RNA-Seq data pipeline called "nf-core/rnaseq" that we can potentially use for processing data in the Pollen PGRP and other related projects.

                For example, the following command shows an example of running this pipeline on a "single end" data set, using a reference genome indicated by the "--fasta" option:

                {code}
                nextflow run nf-core/rnaseq -profile conda --singleEnd --reverseStranded --skipTrimming --reads '*.fastq.gz' --fasta 'ftp://ftp.ensembl.org/pub/release-99/fasta/rattus_norvegicus/dna_index/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz' --gtf 'ftp://ftp.ensembl.org/pub/release-99/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.99.gtf.gz' --fc_count_type transcript
                {code}

                One major benefit of using this pipeline is that there is a lot of support for it in the larger bioinformatics community. There's a company (Sequera) that is supporting this and other Nextflow related projects, and

                		Nextflow provides a standard type of RNA-Seq data pipeline called "nf-core/rnaseq" that we can potentially use for processing data in the Pollen PGRP and other related projects.

                For example, the following command shows an example of running this pipeline on a "single end" data set, using a reference genome indicated by the "--fasta" option:

                {code}
                nextflow run nf-core/rnaseq -profile conda --singleEnd --reverseStranded --skipTrimming --reads '*.fastq.gz' --fasta 'ftp://ftp.ensembl.org/pub/release-99/fasta/rattus_norvegicus/dna_index/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz' --gtf 'ftp://ftp.ensembl.org/pub/release-99/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.99.gtf.gz' --fc_count_type transcript
                {code}

                One major benefit of using this pipeline is that there is a lot of support for it in the larger bioinformatics community. There's a company (Sequera) that is supporting this and other Nextflow related projects.

                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                nfreese Nowlan Freese made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                nfreese Nowlan Freese made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                nfreese Nowlan Freese made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2969 [ IGBF-2969 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2970 [ IGBF-2970 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2971 [ IGBF-2971 ]
                ann.loraine Ann Loraine made changes -
                Epic Link IGBF-2323 [ 18477 ] IGBF-2993 [ 21429 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3143 [ IGBF-3143 ]

                  People

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

                    • Created:
                      Updated:
                      Resolved: