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
- 4.2. Collapsing multiple BED files into a master list by signal
- 4.3. Measuring the frequency of signed distances between SNPs and nearest DHSes
- 4.4. Finding the subset of SNPs within DHSes
- 4.5. Smoothing raw tag count data across the genome
- 4.6. Efficiently creating Starch-formatted archives with a cluster
- 4.7. Working with many input files at once with
bedops
andbedmap