cyberneticlibrary

Execute RNA-seq analysis and quantification pipelines

pipeline-rnaseqskillsetup L4★35

ammawla/encode-toolkit ↗

What it does

Process RNA-seq FASTQ to gene quantification

Best for

Processing bulk RNA-seq from raw data to publication-ready expression matrices following ENCODE standards.

Inputs

· Paired-end FASTQ files
· STAR-indexed reference genome
· Gene annotation GTF

Outputs

· Gene/transcript counts (RSEM)
· BigWig signal tracks
· QC reports (MultiQC)

Requires

· STAR
· RSEM
· Trim Galore
· bedGraphToBigWig
· RSeQC
· MultiQC

Preconditions

· Nextflow DSL2
· Docker or Singularity
· Minimum 30M uniquely mapped reads

Failure modes

· Low mapping rate (<50%)
· High duplication (>50%)
· Strandedness mismatch

Trust signals

· ENCODE uniform analysis standards
· STAR 2-pass mode
· Strand-specific quantification