[mira_talk] Re: fosmid assembly using mira
- From: Rohit Ghai <ghai.rohit@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 23 Dec 2009 20:33:07 +0100
Hi
I am trying a sort of hybrid assembly. Though the mate-pairs are only in
fasta files ( all of them in the same file ).. I have no scf for these
files. I have generated sanger traceinfo file that looks like this..below is
one mate-pair ( different trace_names but same template_id )
<trace>
<trace_name>AFD0ABA46ZH08FM1</trace_name>
<template_id>AFD0ABA46ZH08</template_id>
<clip_vector_left>0</clip_vector_left>
<clip_vector_right>0</clip_vector_right>
<insert_size>35000</insert_size>
<insert_stdev>7000</insert_stdev>
</trace>
<trace>
<trace_name>AFD0ABA46ZH08RM1</trace_name>
<template_id>AFD0ABA46ZH08</template_id>
<clip_vector_left>0</clip_vector_left>
<clip_vector_right>0</clip_vector_right>
<insert_size>35000</insert_size>
<insert_stdev>7000</insert_stdev>
</trace>
The sequences themselves are in a separate fasta file.
The command line is
mira -project=aa -job=denovo,genome,accurate,sanger,454 -GE:not=10
-GE:kcim=yes SANGER_SETTINGS -CL:msvs=yes -ED:ace=yes -LR:mxti=yes
-LR:wqf=no -AS:epoq=no
Mira seems to run nicely but I saw the following in the output
No useful template information found, template routines will not be used.
Also, during the assembly, it mentions how many reads from sanger and 454
have been used for a contig. Several times, I saw more than 2 reads for a
contig. Ideally there should be no more than 2. Is there something wrong
with the way I have specified template information ?
cheers
Rohit
On Wed, Dec 23, 2009 at 1:04 PM, Rohit Ghai <ghai.rohit@xxxxxxxxx> wrote:
> great! will give it a try...
>
>
> On Wed, Dec 23, 2009 at 12:59 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
>
>> On Mittwoch 23 Dezember 2009 Rohit Ghai wrote:
>> > thanks a lot for the new links. The usage is clear in the manual. I am
>> > currently working with MIRA V3rc1 (aka 2.9.48). so the ssaha2 is already
>> > being used in this version or do I have to install the one you have
>> > suggested ?
>>
>> Take the last one, it's not yet present in rc1.
>>
>> > Regardless of your comment that the paired-end section would not help,
>> it
>> > did help a bit in that I realised that I needed to have qual and
>> traceinfo
>> > files for my sanger data, which is essentially the ends of the fosmids
>> we
>> > sequenced. I have only fasta files (no qual etc) ,can I use dummy qual
>> > files ? ( say with a constant quality score of say 40).
>>
>> If none of your Sanger files has qualities, you do not need to generate
>> fake
>> ones.
>>
>> Instead, turn of "wants quality file", set the default quality for Sanger
>> settings to any value you like.
>>
>> SANGER_SETTINGS -LR:wqf=no -AS:bdq=40
>>
>> > I hope the format is alright.
>>
>> If MIRA reads it, then it should be ok.
>>
>> B.
>>
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>
>
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