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.