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.



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. If you have prepared a library yourself and we are just sequencing, please get in touch and mention that you would like us to run this analysis.

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.


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: 18th October 2023

Please read our sample submission instructions before sending samples:

Sample Submission Guidelines
Method Status


We are routinely running this method. Please visit the Order Portal to place an order.

Software tool versions

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Compatible Methods