How to deal with multi mapping reads

Eukaryotic genomes are repetitive in nature i.e. the sequence content is not unique. When mapping high throughput sequencing reads back to the genome, whether for de novo assembly or for RNA sequencing, a subset of reads will map to more than 1 location. Some people refer to these reads as multi-reads for multi mapping reads....

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Equivalents in R, Python and Perl

Last update 2015 September 9th I've been using Perl heavily for several years until I started my PhD back in 2010 (I still use it for many tasks but much more sparingly). Perl was widely used back in the early days when the human genome was yet to be sequenced and this famous article explained...

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