Re: [Seqan-dev] Rabema and RazerS3

[Uwe Appelt <uappelt@clcbio.com>]

On 28/08/2012 09:41, Holtgrewe, Manuel wrote:
> Dear Uwe,
>
> thank you for your email and your questions.
>
> Q1: I just added the -ds option to RazerS 3 yesterday afternoon (Berlin time). Please update your SVN checout.
Excellent! I was using the binaries, available as separate download. 
Building from trunk works and runs fine.

> Q2: Yes, the postprocessing is still required. The reason is that RazerS writes out SAM in the way the standard recommends, omitting the sequence and quality in the SAM records. This saves quite some memory and is fine as long as your SAM is sorted by read name. However, for efficiently building the gold standard, we need a version of the SAM file where the sequence is available in each record and the SAM is sorted by coordinate.
Got it.

> Q3: Thank you for notifying us. This is a typo.
*check*
> HTH,
> Manuel
Yes helped, thanks for your quick 'n' informative reply, Manuel!
Uwe

> ________________________________________
> From: Uwe Appelt [uappelt@clcbio.com]
> Sent: Tuesday, August 28, 2012 9:31 AM
> To: seqan-dev@lists.fu-berlin.de
> Subject: [Seqan-dev] Rabema and RazerS3
>
> 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
>
>
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
>
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev