[mira_talk] Re: fosmid assembly using mira
- From: Rohit Ghai <ghai.rohit@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 23 Dec 2009 12:51:31 +0100
Hi Bastien
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 ?
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).
Regarding the traceinfo files I have managed to cobble up the following for
the fosmid ends...here is a sample...
The sequences in the following example are a mate-pair ( as identified by
the template_id ).
The clip_vector settings are 0, as all clipping has been done before and
there is no vector to clip in these sequences.
I hope the format is alright.
<?xml version="1.0"?>
<trace_volume>
<trace>
<template_id>AFD0ABA49ZH06</template_id>
<trace_name>AFD0ABA49ZH06FM1</trace_name>
<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_end>F</trace_end>
</trace>
<trace>
<template_id>AFD0ABA49ZH06</template_id>
<trace_name>AFD0ABA49ZH06RM1</trace_name>
<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_end>R</trace_end>
</trace>
</trace_volume>
cheers
Rohit
On Wed, Dec 23, 2009 at 11:39 AM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
> On Mittwoch 23 Dezember 2009 Bastien Chevreux wrote:
> > Does the section "Extracting paired-end data from SFF" of the new 454
> usage
> > manual (http://mira-assembler.sourceforge.net/docs/mira_454.html) help?
>
> Vacations! I need vacations. Forget what I wrote, that won't help you a
> bit.
> In fact, I changed usage of SSAHA to SSAHA2 just lately, and the docs for
> that
> haven't made it online yet.
>
> But they're in the latest builds:
>
>
> http://www.chevreux.org/tmp/mira_3rc4e_dev_linux-gnu_x86_64_static.tar.bz2
>
> http://www.chevreux.org/tmp/mira_3rc4e_dev_linux-gnu_i686_32_static.tar.bz2
> http://www.chevreux.org/tmp/mira-3rc4e.tar.bz2
> http://www.chevreux.org/tmp/mira_3rdparty_21-12-2009.tar.bz2
>
> Look in the "usage" manual for the section "Using SSAHA2 to screen for
> vector
> sequence"
>
> B.
>
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