Examples from the Wild I: REGULAR EXPRESSIONS

NGS Analysis of ChIP-seq data with NUCwave

ChIP-Seq example at NUCwave site

S. cerevisiae reference genome was downloaded from SGD and FASTA headers for chromosome names were replaced with chrI-chrXVI.

Of course, there are only sixteen chromosomes in yeast, plus the mitochondrial genome, so this is not an overly difficult to do by hand. But it is tedious and offers a good place to utilize regular expressions.

Highly recommend the following combination for learning Regular Expressions, or Regex or Regexp as it is often called:

• Chapters 2 & 3 of Practical Computing for Biologists book by Haddock and Dunn. The related appendix #2 is freely available as part of tables of Appendices from Practical Computing for Biologists book by Haddock and Dunn
• Regular Expressions Primer
• Regular Expressions 101: online regex editor and debugger tool (This seems best with g global modifier on.)

First I’ll demonstrate doing this with Sublime Text using the process I already worked out.

So what are Regular Expressions? See Exploring with Regular Expressions 101.

I’ll demo wildcards, character sets, qantifiers and capturing.

Finally, we’ll use Regular Expressions 101 to really follow what was going on in this example.