​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 reads (fastq files)
  
  
• Mapping short reads
  
  
• SAM/BAM summarizing and processing
  
  
• SAM/BAM quality control
  
  
• Using ChIP-Seq to identify and/or quantify bound regions (peaks)
  
  
• to make stacked heatmaps and profiles of genes or genomic regions (like ChIP-seq 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
  
  
• Creating genome feature heatmaps from sequencing experiments
  
  
• Creating an analysis pipeline of compressed files
  
  

Variant calling and analysis

• Using Samtools' mpileup/bcftools to call variants from short-read sequencing
  
  
• Using GATK to call variants from short-read sequencing
  
  
• Calling variants from RNA-seq data
  
  
• 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
  
  
• Searching for patterns or motifs in a DNA or protein sequence
  
  
• Clustering a matrix and creating a heatmap
  
  
• ChIP-Seq analysis bake-off results
  
  

In Progress

• Experimental design of short read sequencing experiments
  
  
• Mass spectrometry data analysis