From e3d7c26c9800aec8709d4ef81bc49b571c098e2a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Steffen=20M=C3=B6ller?= Date: Thu, 13 Jul 2023 17:06:51 +0200 Subject: [PATCH 1/2] README.md: Pointer to downstream workflow 'differential abundance' --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index 31314a457..7ff5dfaa1 100644 --- a/README.md +++ b/README.md @@ -95,6 +95,8 @@ To see the results of an example test run with a full size dataset refer to the For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/rnaseq/output). +This pipeline assigns the RNA/cDNA reads to genes in the genome, counts the number of reads per gene and normalizes the data. It does not compare the samples or assign P values to individual genes. For downstream analyses, the output files can be analysed directly in statistics environments like [R](https://www.r-project.org/) or [Julia](https://julialang.org/), or be forwarded to another workflow of Nextflow to determine transcripts with [differential abundance](https://github.com/nf-core/differentialabundance/). + ## Online videos A short talk about the history, current status and functionality on offer in this pipeline was given by Harshil Patel ([@drpatelh](https://github.com/drpatelh)) on [8th February 2022](https://nf-co.re/events/2022/bytesize-32-nf-core-rnaseq) as part of the nf-core/bytesize series. From a55caf0580763d9330d0c4ef49c87f7a3d3c3339 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Wed, 2 Aug 2023 23:12:08 +0200 Subject: [PATCH 2/2] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 7ff5dfaa1..4ac07704e 100644 --- a/README.md +++ b/README.md @@ -95,7 +95,7 @@ To see the results of an example test run with a full size dataset refer to the For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/rnaseq/output). -This pipeline assigns the RNA/cDNA reads to genes in the genome, counts the number of reads per gene and normalizes the data. It does not compare the samples or assign P values to individual genes. For downstream analyses, the output files can be analysed directly in statistics environments like [R](https://www.r-project.org/) or [Julia](https://julialang.org/), or be forwarded to another workflow of Nextflow to determine transcripts with [differential abundance](https://github.com/nf-core/differentialabundance/). +This pipeline quantifies RNA-sequenced reads relative to genes/transcripts in the genome and normalizes the resulting data. It does not compare the samples statistically in order to assign significance in the form of FDR or P-values. For downstream analyses, the output files from this pipeline can be analysed directly in statistical environments like [R](https://www.r-project.org/), [Julia](https://julialang.org/) or via the [nf-core/differentialabundance](https://github.com/nf-core/differentialabundance/) pipeline. ## Online videos