RNA-seq analysis
Runs with illumina total RNA-sequencing data. Aligns to the reference genome, gives QC metrics and finishes with gene count matrices.
RNA-Seq is a bioinformatics analysis pipeline used for RNA sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It processes raw data from FastQ inputs, aligns the reads, generates counts relative to genes or transcripts and performs extensive quality control on the results.
nf-core/rnaseq
https:
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. - https://nf-co.re/rnaseq
When we run analysis
We run this analysis routinely for all RNA-seq projects where we have prepared the sequencing library in-house. The analysis works with any of the species that have a reference genome available in AWS-iGenomes. If in doubt, please ask whether we can run the pipeline for you.
Input data
bcl2fastq demultiplexed FastQ files and a genome reference.
Results
The pipeline generates aligned BAM-files, gene count matrices and FPKM metrics for genes and transcripts, along with numerous quality control metrics. For more information, please see https://nf-co.re/rnaseq/[release]/docs/output
Last Updated: 12th November 2024