Common Sequence Analysis Work Flows

Martin Morgan, Sonali Arora
October 28, 2014

RNA-seq

See the lecture notes and lab.

RNA-seq differential expression of known genes

RNA-seq differential expression of known transcripts

Single-cell expression

ChIP-seq

See my recent slides outlining ChIP-seq and relevant Bioconductor software.

Copy Number

See the Copy Number Workflow document.

Variants

See Michael Lawrence's variant calling with VariantTools. and Val Obenchain's manipulation and annotation of called variants with VariantAnnotation.

Epigenomics

See the short introduction and lab centered around Illumina 450k methylation arrays and the minfi package.

Microbiome