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 2018 May 24th Perl was used by many computational biologists back in early 2000. The popularity of Perl may have been driven by its involvement with the human genome project. An article titled “How Perl Saved the Human Genome Project” explains why Perl was a good fit for computational biology projects (as well…

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