Friday, 15 July 2011

WGsim and bowtie paired end mapping

I wanted to simulate PE reads with wgsim but by using the default params, i didn't realise that I was creating reads with 500 bp insert. which doesn't go well with Bowtie's PE default of 250 bp which to cut a long story short, resulted in low pairing rates.

Only found this out by googling biostar  of course there is the obligatory discussion of merits of using bowtie versus bwa or vice versa. and there are some nice graphs in there that illustrate the problem at hand.

1 comment:

  1. Ryan Cunningham14 March 2012 at 05:45

    Thank you SO much for posting this! I had exactly the same problem, and I would've wasted hours debugging it if you hadn't posted this.


Datanami, Woe be me