Re: [wgs-assembler-users] S. purpuratus parameters

[mathog <ma...@ca...>]

Three of the four Illumina data sets used are "Nextera Mate Pair Reads", 
but
the frg files for those differ from the other one only in library and 
file names, and this:

< mea:1000.000
< std:100.000
---
> mea:3000.000
> std:300.000

These mate pair reads were described as "innie" in the frg files, but 
with respect to the source DNA, I'm thinking now they probably should 
have been "outie".  Or maybe not, since there is supposed to be code to 
detect and handle these:

http://wgs-assembler.sourceforge.net/wiki/index.php/Pair_classification_within_Illumina_mate_pair_data

Does the analysis described in the preceding link occur automatically 
for Illumina data, or is something special needed to turn it on?

Thanks,

David Mathog
ma...@ca...
Manager, Sequence Analysis Facility, Biology Division, Caltech