useful_links.md

Useful links

Read processing/alignment

• cutadapt, for trimming reads
• STAR aligner, for aligning reads to a reference
• htseq-count, for quantifying read counts at genomic features

Quality control

• Picard tools, including CollectRnaSeqMetrics
• FastQC, for basic FASTQ quality control
• MultiQC, for aggregating quality control reports

Differential expression

• DESeq2, original manuscript: Love et al, 2014
• tximport, original manuscript: Soneson et al, 2014
• edgeR, original manuscript: Robinson et al, 2010
• limma, original manuscript: Ritchie et al, 2015
• limma-voom

Other

• Conda
• Introduction to RNA-Seq using high-performance computing, workshop by Harvard Chan Bioinformatics Core