Re: [wgs-assembler-users] Erroneous ASM file

[Mayank M. <may...@ic...>]

Hej Brian,
wow! I was stuck for three weeks with this consensus problem. Thats called extreme bad luck. 

But have you check the GC content with the latest version. because when I calculate it from the scf.fasta its 2% higher than what the caqc.pl shows me.  

Also, usually celera gives very stable assemblies when you do no change the data and parameters. But the new version is giving me a bit different assemblies. It seems that these builds are not completely reliable. Can you guide me which build I must choose and how to download it. 

WarmRegards,
Mayank

On 30 sep 2013, at 15:04, "Walenz, Brian" <bw...@jc...> wrote:

> Dang, I think you might have hit a stupid bug I introduced and then fixed
> much later than I'm happy to admit.
> 
> Broken in this:
> 
> r4393 | brianwalenz | 2013-08-24 03:46:56 -0400 (Sat, 24 Aug 2013) | 2 lines
> Add runCA option cgwPreserveConsensus.
> 
> Fixed in this:
> 
> r4406 | brianwalenz | 2013-09-06 18:42:08 -0400 (Fri, 06 Sep 2013) | 3 lines
> The cgwPreserveConsensus default value was incorrect resulting in cgw always
> retaining the consensus sequence, and 8-consensus never recomputing it.
> 
> Does 'svn info' show a revision between those two?
> 
> 
> 
> On 9/30/13 8:12 AM, "Mayank Mahajan" <may...@ic...> wrote:
> 
>> Hello,
>> I have been using the unstable release of WGS assembler. I have some
>> really good assemblies as per my post assembly checks.
>> The problem is that the {CCO tags in the asm file are all loosing the
>> information whenever they have more than one unitig in the contig.
>> Whenever there is more than one unitig in the contig the quality
>> values of the whole consensus just become zero. The contigs loose all
>> the gap information which takes into consideration the indels in the
>> reads. And respectively, all the reads also loose the indel
>> information in the contigs.
>> 
>> Regards,
>> Mayank Mahajan
>