Documentation

[Sven Klages]

Hi,

is there a current (2.1) manual? 1.0 is a bit outdated ...

I am looking for info on "-ann(pe|se) <Neural network filename>".

thanks,
Sven

[Wan-Ping Lee]

Hi Sven,

If you're looking for the files, then they should be in src/networkFile. If you're interested in the idea about them, Here is the description about it.

MOSAIK’s mapping qualities are obtained by the neural network that approximates the error function provided features such as best and second best Smith-Waterman scores, entropies of reads, numbers of obtained mappings and hashes. For paired-end reads, the fragment length between mates of a pair is taken into account for more precise mapping quality calculation. MOSAIK embeds Fast Artificial Neural Network (FANN) library (http://leenissen.dk/fann/wp/), which implements multilayer artificial neural networks in C with supporting both fully connected and sparsely connected networks, to calculate Phred score for each alignment.

Best,

Wan-Ping Lee

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Wan-Ping Lee
Postdoctoral Research Associate
Department of Biology, Boston College

Tel: +1 (617) 552-2922
wanpi...@bc.edu