[mira_talk] Re: paired_end

Hi Jan,

On 14 Apr 2009, at 16:08 , Jan Paces wrote:


Unfortunately it looks like it
is not possible to download .sff files from NCBI trace archive anymore, 
they are offering only fasta or fastq
You can access some of them via ftp, but I don't know how long it's going to last: 
ftp://ftp.ncbi.nih.gov/pub/TraceDB/ShortRead/


 I know rns parameter, but how to set up
insert size?
I think there are some other utilities in the third-party tools of mira, although I don't know how they work. AFAIK, I have split my reads, using .r and .f suffixes. The xml file then resembles: 

<?xml version="1.0"?>
<trace_volume>
    <trace>
        <trace_name>FLVI58L05FSYNS.r</trace_name>
        <insert_stdev>3000</insert_stdev>
        <insert_size>20000</insert_size>
        <clip_vector_right>94</clip_vector_right>
        <template_id>FLVI58L05FSYNS</template_id>
        <trace_end>r</trace_end>
    </trace>
    <trace>
        <trace_name>FLVI58L05FSYNS.f</trace_name>
        <insert_stdev>3000</insert_stdev>
        <insert_size>20000</insert_size>
        <clip_vector_right>62</clip_vector_right>
        <template_id>FLVI58L05FSYNS</template_id>
        <trace_end>f</trace_end>
    </trace>
...
</trace_volume>

Hope that helps...

Lionel

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