4. Usage examples

The following examples demonstrate the use of BEDOPS in analyzing genomic data. Here, we provide source code and snippets of data to demonstrate “real-world” examples based on daily usage of these tools in the Stamatoyannopoulos lab.

• 4.1. Visualizing the relationship of SNPs and generic genomic features
  • 4.1.1. BEDOPS tools in use
  • 4.1.2. Script
  • 4.1.3. Discussion
  • 4.1.4. Downloads
• 4.2. Collapsing multiple BED files into a master list by signal
  • 4.2.1. BEDOPS tools in use
  • 4.2.2. Script
  • 4.2.3. Discussion
• 4.3. Measuring the frequency of signed distances between SNPs and nearest DHSes
  • 4.3.1. BEDOPS tools in use
  • 4.3.2. Script
  • 4.3.3. Discussion
  • 4.3.4. Downloads
• 4.4. Finding the subset of SNPs within DHSes
  • 4.4.1. BEDOPS tools in use
  • 4.4.2. Script
  • 4.4.3. Discussion
  • 4.4.4. Downloads
• 4.5. Smoothing raw tag count data across the genome
  • 4.5.1. BEDOPS tools in use
  • 4.5.2. Script
• 4.6. Efficiently creating Starch-formatted archives with a cluster
  • 4.6.1. BEDOPS tools in use
  • 4.6.2. Script
  • 4.6.3. Discussion
    • 4.6.3.1. Splitting BED files
    • 4.6.3.2. Compressing BED subsets
    • 4.6.3.3. Stitching together compressed sets
• 4.7. Working with many input files at once with bedops and bedmap
  • 4.7.1. Discussion