nf-core/rnaseq: RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Introduction nf-core/rnaseq is a bioinformatics pipeline that can be used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet with FASTQ files or pre-aligned BAM files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expression matrix and extensive QC report. In case the image above is not loading, please have a look at the static version. Merge re-sequenced FastQ files (cat) Auto-infer strandedness by subsampling and pseudoalignment (fq, Salmon) Read QC (FastQC) UMI…

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• Hannah Le

related reading

• rnaseq: Parametersnf-co.re
• A survey of best practices for RNA-seq data analysisgenomebiology.biomedcentral.com
• GitHub - BioDepot/RNA-seq-lambda: Rapid RNA-seq pipeline using AWS lambda functions for alignmentgithub.com
• Using prototyping to choose a bioinformatics workflow management system | PLOS Computational Biologyjournals.plos.org
• Signature-scoring methods developed for bulk samples are not adequate for cancer single-cell RNA sequencing data | eLifeelifesciences.org
• Identifying and mitigating batch effects in whole genome sequencing databmcbioinformatics.biomedcentral.com
• Transcriptome assemblynbisweden.github.io
• Peak calling with MACS2 | Introduction to ChIP-Seq using high-performance computinghbctraining.github.io
• Advancing regulatory variant effect prediction with AlphaGenomenature.com
• Somatic mutation landscapes at single-molecule resolutionnature.com
• GitHub - harvardnlp/annotated-transformer: An annotated implementation of the Transformer paper. · GitHubgithub.com
• GitHub - Illumina/SpliceAI: A deep learning-based tool to identify splice variantsgithub.com