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Workflow

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This workflow performs differential expression analysis on single- or paired-end RNA-seq data. -After adapter removal with Cutadapt, reads were mapped and gene counts were generated with STAR. -Gene counts of replicated were summed up. -Integrated normalization and differential expression analysis was conducted with DESeq2 following standard procedure as outlined in the manual.

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Detailed software versions can be found under Rules

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Results

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pca.svg

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Principal component analysis over the normalized counts of all genes.

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treated-vs-untreated.diffexp.tsv

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Table of differential expression results for per gene calculated with DESeq2.

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treated-vs-untreated.ma-plot.svg

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MA plot of log fold change vs. mean of normalized counts for each gene when calculating differential expression for contrast treated-vs-untreated.

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Statistics

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- If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue. -
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Rules

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RuleJobsOutputSingularityConda environment
deseq21 - -
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    - -
  • results/diffexp/treated-vs-untreated.diffexp.tsv
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  • results/diffexp/treated-vs-untreated.ma-plot.svg
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    - -
  • r-base =3.4.1
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  • bioconductor-deseq2 =1.18.1
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  • bioconductor-annotate =1.56.0
  • - -
  • bioconductor-annotationdbi =1.40.0
  • - -
  • bioconductor-biobase =2.38.0
  • - -
  • bioconductor-biocgenerics =0.24.0
  • - -
  • bioconductor-biocparallel =1.12.0
  • - -
  • bioconductor-delayedarray =0.4.1
  • - -
  • bioconductor-genefilter =1.60.0
  • - -
  • bioconductor-geneplotter =1.56.0
  • - -
  • bioconductor-genomeinfodb =1.14.0
  • - -
  • bioconductor-genomeinfodbdata =1.0.0
  • - -
  • bioconductor-genomicranges =1.30.0
  • - -
  • bioconductor-iranges =2.12.0
  • - -
  • bioconductor-s4vectors =0.16.0
  • - -
  • bioconductor-summarizedexperiment =1.8.0
  • - -
  • bioconductor-tximport =1.6.0
  • - -
  • bioconductor-xvector =0.18.0
  • - -
  • bioconductor-zlibbioc =1.24.0
  • - -
  • r-acepack =1.4.1
  • - -
  • r-backports =1.0.5
  • - -
  • r-base64enc =0.1_3
  • - -
  • r-bh =1.65.0_1
  • - -
  • r-bit =1.1_12
  • - -
  • r-bit64 =0.9_5
  • - -
  • r-bitops =1.0_6
  • - -
  • r-blob =1.1.0
  • - -
  • r-catools =1.17.1
  • - -
  • r-checkmate =1.8.2
  • - -
  • r-cluster =2.0.6
  • - -
  • r-colorspace =1.3_2
  • - -
  • r-dbi =0.6_1
  • - -
  • r-dichromat =2.0_0
  • - -
  • r-digest =0.6.12
  • - -
  • r-evaluate =0.10
  • - -
  • r-foreign =0.8_67
  • - -
  • r-formula =1.2_1
  • - -
  • r-futile.logger =1.4.3
  • - -
  • r-futile.options =1.0.0
  • - -
  • r-gdata =2.17.0
  • - -
  • r-getopt =1.20.0
  • - -
  • r-ggplot2 =2.2.0
  • - -
  • r-gplots =3.0.1
  • - -
  • r-gridextra =2.2.1
  • - -
  • r-gtable =0.2.0
  • - -
  • r-gtools =3.5.0
  • - -
  • r-highr =0.6
  • - -
  • r-hmisc =4.0_3
  • - -
  • r-htmltable =1.9
  • - -
  • r-htmltools =0.3.6
  • - -
  • r-htmlwidgets =0.9
  • - -
  • r-jsonlite =1.4
  • - -
  • r-kernsmooth =2.23_15
  • - -
  • r-knitr =1.16
  • - -
  • r-labeling =0.3
  • - -
  • r-lambda.r =1.1.9
  • - -
  • r-lattice =0.20_34
  • - -
  • r-latticeextra =0.6_28
  • - -
  • r-lazyeval =0.2.0
  • - -
  • r-locfit =1.5_9.1
  • - -
  • r-magrittr =1.5
  • - -
  • r-markdown =0.8
  • - -
  • r-mass =7.3_45
  • - -
  • r-matrix =1.2_7.1
  • - -
  • r-matrixstats =0.52.2
  • - -
  • r-memoise =1.1.0
  • - -
  • r-mime =0.5
  • - -
  • r-munsell =0.4.3
  • - -
  • r-nnet =7.3_12
  • - -
  • r-pkgconfig =2.0.1
  • - -
  • r-plogr =0.1_1
  • - -
  • r-plyr =1.8.4
  • - -
  • r-rcolorbrewer =1.1_2
  • - -
  • r-rcpp =0.12.13
  • - -
  • r-rcpparmadillo =0.7.800.2.0
  • - -
  • r-rcurl =1.95_4.8
  • - -
  • r-reshape2 =1.4.2
  • - -
  • r-rjson =0.2.15
  • - -
  • r-rlang =0.1.2
  • - -
  • r-rpart =4.1_10
  • - -
  • r-rsqlite =2.0
  • - -
  • r-scales =0.4.1
  • - -
  • r-snow =0.4_2
  • - -
  • r-stringi =1.1.2
  • - -
  • r-stringr =1.2.0
  • - -
  • r-survival =2.40_1
  • - -
  • r-tibble =1.3.3
  • - -
  • r-viridis =0.4.0
  • - -
  • r-viridislite =0.2.0
  • - -
  • r-xml =3.98_1.6
  • - -
  • r-xtable =1.8_2
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  • r-yaml =2.1.14
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pca1 - -
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    - -
  • results/pca.svg
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-
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-
    - -
  • r-base =3.4.1
  • - -
  • bioconductor-deseq2 =1.18.1
  • - -
  • bioconductor-annotate =1.56.0
  • - -
  • bioconductor-annotationdbi =1.40.0
  • - -
  • bioconductor-biobase =2.38.0
  • - -
  • bioconductor-biocgenerics =0.24.0
  • - -
  • bioconductor-biocparallel =1.12.0
  • - -
  • bioconductor-delayedarray =0.4.1
  • - -
  • bioconductor-genefilter =1.60.0
  • - -
  • bioconductor-geneplotter =1.56.0
  • - -
  • bioconductor-genomeinfodb =1.14.0
  • - -
  • bioconductor-genomeinfodbdata =1.0.0
  • - -
  • bioconductor-genomicranges =1.30.0
  • - -
  • bioconductor-iranges =2.12.0
  • - -
  • bioconductor-s4vectors =0.16.0
  • - -
  • bioconductor-summarizedexperiment =1.8.0
  • - -
  • bioconductor-tximport =1.6.0
  • - -
  • bioconductor-xvector =0.18.0
  • - -
  • bioconductor-zlibbioc =1.24.0
  • - -
  • r-acepack =1.4.1
  • - -
  • r-backports =1.0.5
  • - -
  • r-base64enc =0.1_3
  • - -
  • r-bh =1.65.0_1
  • - -
  • r-bit =1.1_12
  • - -
  • r-bit64 =0.9_5
  • - -
  • r-bitops =1.0_6
  • - -
  • r-blob =1.1.0
  • - -
  • r-catools =1.17.1
  • - -
  • r-checkmate =1.8.2
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  • r-cluster =2.0.6
  • - -
  • r-colorspace =1.3_2
  • - -
  • r-dbi =0.6_1
  • - -
  • r-dichromat =2.0_0
  • - -
  • r-digest =0.6.12
  • - -
  • r-evaluate =0.10
  • - -
  • r-foreign =0.8_67
  • - -
  • r-formula =1.2_1
  • - -
  • r-futile.logger =1.4.3
  • - -
  • r-futile.options =1.0.0
  • - -
  • r-gdata =2.17.0
  • - -
  • r-getopt =1.20.0
  • - -
  • r-ggplot2 =2.2.0
  • - -
  • r-gplots =3.0.1
  • - -
  • r-gridextra =2.2.1
  • - -
  • r-gtable =0.2.0
  • - -
  • r-gtools =3.5.0
  • - -
  • r-highr =0.6
  • - -
  • r-hmisc =4.0_3
  • - -
  • r-htmltable =1.9
  • - -
  • r-htmltools =0.3.6
  • - -
  • r-htmlwidgets =0.9
  • - -
  • r-jsonlite =1.4
  • - -
  • r-kernsmooth =2.23_15
  • - -
  • r-knitr =1.16
  • - -
  • r-labeling =0.3
  • - -
  • r-lambda.r =1.1.9
  • - -
  • r-lattice =0.20_34
  • - -
  • r-latticeextra =0.6_28
  • - -
  • r-lazyeval =0.2.0
  • - -
  • r-locfit =1.5_9.1
  • - -
  • r-magrittr =1.5
  • - -
  • r-markdown =0.8
  • - -
  • r-mass =7.3_45
  • - -
  • r-matrix =1.2_7.1
  • - -
  • r-matrixstats =0.52.2
  • - -
  • r-memoise =1.1.0
  • - -
  • r-mime =0.5
  • - -
  • r-munsell =0.4.3
  • - -
  • r-nnet =7.3_12
  • - -
  • r-pkgconfig =2.0.1
  • - -
  • r-plogr =0.1_1
  • - -
  • r-plyr =1.8.4
  • - -
  • r-rcolorbrewer =1.1_2
  • - -
  • r-rcpp =0.12.13
  • - -
  • r-rcpparmadillo =0.7.800.2.0
  • - -
  • r-rcurl =1.95_4.8
  • - -
  • r-reshape2 =1.4.2
  • - -
  • r-rjson =0.2.15
  • - -
  • r-rlang =0.1.2
  • - -
  • r-rpart =4.1_10
  • - -
  • r-rsqlite =2.0
  • - -
  • r-scales =0.4.1
  • - -
  • r-snow =0.4_2
  • - -
  • r-stringi =1.1.2
  • - -
  • r-stringr =1.2.0
  • - -
  • r-survival =2.40_1
  • - -
  • r-tibble =1.3.3
  • - -
  • r-viridis =0.4.0
  • - -
  • r-viridislite =0.2.0
  • - -
  • r-xml =3.98_1.6
  • - -
  • r-xtable =1.8_2
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  • r-yaml =2.1.14
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deseq2_init1 - -
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    - -
  • deseq2/all.rds
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-
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    - -
  • r-base =3.4.1
  • - -
  • bioconductor-deseq2 =1.18.1
  • - -
  • bioconductor-annotate =1.56.0
  • - -
  • bioconductor-annotationdbi =1.40.0
  • - -
  • bioconductor-biobase =2.38.0
  • - -
  • bioconductor-biocgenerics =0.24.0
  • - -
  • bioconductor-biocparallel =1.12.0
  • - -
  • bioconductor-delayedarray =0.4.1
  • - -
  • bioconductor-genefilter =1.60.0
  • - -
  • bioconductor-geneplotter =1.56.0
  • - -
  • bioconductor-genomeinfodb =1.14.0
  • - -
  • bioconductor-genomeinfodbdata =1.0.0
  • - -
  • bioconductor-genomicranges =1.30.0
  • - -
  • bioconductor-iranges =2.12.0
  • - -
  • bioconductor-s4vectors =0.16.0
  • - -
  • bioconductor-summarizedexperiment =1.8.0
  • - -
  • bioconductor-tximport =1.6.0
  • - -
  • bioconductor-xvector =0.18.0
  • - -
  • bioconductor-zlibbioc =1.24.0
  • - -
  • r-acepack =1.4.1
  • - -
  • r-backports =1.0.5
  • - -
  • r-base64enc =0.1_3
  • - -
  • r-bh =1.65.0_1
  • - -
  • r-bit =1.1_12
  • - -
  • r-bit64 =0.9_5
  • - -
  • r-bitops =1.0_6
  • - -
  • r-blob =1.1.0
  • - -
  • r-catools =1.17.1
  • - -
  • r-checkmate =1.8.2
  • - -
  • r-cluster =2.0.6
  • - -
  • r-colorspace =1.3_2
  • - -
  • r-dbi =0.6_1
  • - -
  • r-dichromat =2.0_0
  • - -
  • r-digest =0.6.12
  • - -
  • r-evaluate =0.10
  • - -
  • r-foreign =0.8_67
  • - -
  • r-formula =1.2_1
  • - -
  • r-futile.logger =1.4.3
  • - -
  • r-futile.options =1.0.0
  • - -
  • r-gdata =2.17.0
  • - -
  • r-getopt =1.20.0
  • - -
  • r-ggplot2 =2.2.0
  • - -
  • r-gplots =3.0.1
  • - -
  • r-gridextra =2.2.1
  • - -
  • r-gtable =0.2.0
  • - -
  • r-gtools =3.5.0
  • - -
  • r-highr =0.6
  • - -
  • r-hmisc =4.0_3
  • - -
  • r-htmltable =1.9
  • - -
  • r-htmltools =0.3.6
  • - -
  • r-htmlwidgets =0.9
  • - -
  • r-jsonlite =1.4
  • - -
  • r-kernsmooth =2.23_15
  • - -
  • r-knitr =1.16
  • - -
  • r-labeling =0.3
  • - -
  • r-lambda.r =1.1.9
  • - -
  • r-lattice =0.20_34
  • - -
  • r-latticeextra =0.6_28
  • - -
  • r-lazyeval =0.2.0
  • - -
  • r-locfit =1.5_9.1
  • - -
  • r-magrittr =1.5
  • - -
  • r-markdown =0.8
  • - -
  • r-mass =7.3_45
  • - -
  • r-matrix =1.2_7.1
  • - -
  • r-matrixstats =0.52.2
  • - -
  • r-memoise =1.1.0
  • - -
  • r-mime =0.5
  • - -
  • r-munsell =0.4.3
  • - -
  • r-nnet =7.3_12
  • - -
  • r-pkgconfig =2.0.1
  • - -
  • r-plogr =0.1_1
  • - -
  • r-plyr =1.8.4
  • - -
  • r-rcolorbrewer =1.1_2
  • - -
  • r-rcpp =0.12.13
  • - -
  • r-rcpparmadillo =0.7.800.2.0
  • - -
  • r-rcurl =1.95_4.8
  • - -
  • r-reshape2 =1.4.2
  • - -
  • r-rjson =0.2.15
  • - -
  • r-rlang =0.1.2
  • - -
  • r-rpart =4.1_10
  • - -
  • r-rsqlite =2.0
  • - -
  • r-scales =0.4.1
  • - -
  • r-snow =0.4_2
  • - -
  • r-stringi =1.1.2
  • - -
  • r-stringr =1.2.0
  • - -
  • r-survival =2.40_1
  • - -
  • r-tibble =1.3.3
  • - -
  • r-viridis =0.4.0
  • - -
  • r-viridislite =0.2.0
  • - -
  • r-xml =3.98_1.6
  • - -
  • r-xtable =1.8_2
  • - -
  • r-yaml =2.1.14
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count_matrix1 - -
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    - -
  • counts/all.tsv
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align3 - -
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    - -
  • star/B-2/Aligned.out.bam
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  • star/B-2/ReadsPerGene.out.tab
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  • star/A-1/Aligned.out.bam
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  • star/A-1/ReadsPerGene.out.tab
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  • star/B-1/Aligned.out.bam
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  • star/B-1/ReadsPerGene.out.tab
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-
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-
    - -
  • star ==2.5.3a
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-
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cutadapt1 - -
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    - -
  • trimmed/B-2.fastq.gz
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  • trimmed/B-2.qc.txt
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-
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-
    - -
  • cutadapt ==1.13
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cutadapt_pe2 - -
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    - -
  • trimmed/A-1.1.fastq.gz
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  • trimmed/A-1.2.fastq.gz
  • - -
  • trimmed/A-1.qc.txt
  • - -
  • trimmed/B-1.1.fastq.gz
  • - -
  • trimmed/B-1.2.fastq.gz
  • - -
  • trimmed/B-1.qc.txt
  • - -
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-
- - -
-
    - -
  • cutadapt ==1.13
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-
- -
-