​BaRC Standard operating procedures

These are "how-to's" detailing the methods that BaRC uses and finds to work effectively. Email BaRC if you have any questions about how or why to perform what is described on these pages.

Short read sequencing

• Quality control and preprocessing of short-read sequencing
  
  
• Mapping short reads
  
  
• Using ChIP-Seq to identify and/or quantify bound regions (peaks)
  
  
• Using RNA-Seq to quantify gene levels and assay for differential expression
  
  
• Using RNA-Seq to assemble or annotate transcripts
  
  
• Integrating expression and immunoprecipitation experiments
  
  
• Summarizing, mining, and processing SAM/BAM files
  
  
• Creating genome feature heatmaps from sequencing experiments
  
  
• Creating an analysis pipeline of compressed files
  
  

Variant calling and analysis

• Calling variants from short-read sequencing
  
  
• Using GATK to call variants from short-read sequencing
  
  
• Manipulating VCF files
  
  
• Interpreting VCF files
  
  

Genome coordinates and genomics

• Creating genome coordinate files (bed, wig, etc) for genome browsers
  
  
• Linking genome regions to genome annotation(s)
  
  
• Extracting genome subsequences
  
  
• Identifying homologous genes/proteins
  
  

Microarrays

• Normalizing and preprocessing microarrays
  
  
• Identifying differentially expressed genes from microarrays
  
  
• Normalizing multiple public microarray datasets
  
  

Enrichment analysis

• Identifying all and/or enriched transcription factor binding sites
  
  
• Identifying enriched GO or other annotation terms in a set of genes
  
  

Statistics

• Performing and reporting statistical tests
  
  
• Calculating variation (SD, SE) for a ratio
  
  
• Performing ANOVA in R
  
  

Other topics

• Producing a multiple sequence alignment of proteins, transcripts, or genome regions
  
  
• Clustering a matrix and creating a heatmap
  
  
• ChIP-Seq analysis bake-off results
  
  

In Progress