[mira_talk] Re: BAC vector sequece masking for de novo assembly using PacBio C2
- From: Juan Pascual Anaya <jpascualanaya@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 12 Dec 2013 19:03:56 +0900
Well, it took just few hours to finish (well, my BACs comprise only 1.8Mb).
Now playing with the output. Since it is fast, I will be tweaking the
parameters until I get optimal results.
Thanks a lot for your help Bastien!!
Juan
On Wed, Dec 11, 2013 at 12:45 PM, Juan Pascual Anaya <
jpascualanaya@xxxxxxxxx> wrote:
> There we go! I'll let you know when my computer explodes!
>
> Thank you very much for all your help!!
> Champi
>
>
> On Tue, Dec 10, 2013 at 11:07 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
>
>> > On December 10, 2013 at 2:36 PM Juan Pascual Anaya <
>> jpascualanaya@xxxxxxxxx>
>> > wrote:
>> > I am sort of scared to increase the -SK:mmhr... although I have seen in
>> other
>> > posts that it can be set
>> > to 100 if one wants the repeats also assembled... like in my case (so I
>> should
>> > use then -HS:mnr=off).
>>
>> Yes, simply turn off -HS:mnr and increase -SK:mmhr to 100. No reason to be
>> scafred, your computer won't undergo a nuclear meltdown or such. Though
>> your
>> disk might, but you'd find out soon enough if the assembly takes ages.
>>
>> B.
>>
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>
>
>
> --
>
> Juan Pascual-Anaya, PhD
> Research Scientist
> Laboratory for Evolutionary Morphology
> Center for Developmental Biology (CDB) RIKEN
> 2-2-3 Minatojima-minamimachi
> Chuo-ku, Kobe, Hyogo 650-0047
> Japan
>
--
Juan Pascual-Anaya, PhD
Research Scientist
Laboratory for Evolutionary Morphology
Center for Developmental Biology (CDB) RIKEN
2-2-3 Minatojima-minamimachi
Chuo-ku, Kobe, Hyogo 650-0047
Japan
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