[Seqan-dev] Rabema and RazerS3

[Uwe Appelt <uappelt@clcbio.com>]

Hi @All.

Liking Rabema, I appreciated the release of RazerS3 and the updates to 
the Rabema-manual (on http://www.seqan.de/projects/rabema/manual/).

Q1) So to produce a golden standard we would execute the following 
command (as given in step 1A):

razers3 -v -of sam -rr 100 -i 92 -m 1000000 -ds -o gold_pre.sam 
genome.fa reads.fq

This is however imprecisely updated, because the "-ds" option does seem 
to exist in razers3 ("razers3: illegal option --ds"). I assume, I can 
just omit the "-ds"?

Q2) In step 1b, postprocessing of the razers3-sam output is described, 
does that still apply?

Q3) Just a minor thing: in step (1A) you use an identity value of 92%, 
while you describe 6% to be the corresponding error rate in step (2). 
That's just a typo, I guess?!

Thanks in advance,
Uwe