[mira_talk] Re: Subject: De-novo hybrid assemblies ( Solexa + ...)

Nobody know the answer of my problem?
Is it too confusing?
After run 454 reads by using MIRA and BAMBUS, I extract the longest scaffold
and treat it as a backbone. I hope that I able to polish this longest
scaffold by using Illumina reads to get better assembly result.
I just confusing how to use MIRA to polish my longest scaffold and get
better assembly result.
Thanks again for everybody.

best regards
edge


On Fri, Oct 16, 2009 at 9:45 AM, Chia Jing Yi <cjyxiaodi1@xxxxxxxxx> wrote:

> Thanks a lot, Bastien.
> I feel a bit confusing at the part of "Mapping assemblies" and "De-novo
> hybrid assemblies"
> For example, I got a bacteria genome which sequencing by 454 technique and
> Illumina technique separately.
>
> For 454 technique read (included standard and paired-end sff file),
> I follow the "Instructions of scaffolding MIRA 454 contigs & 25KB
> paired-end data with BAMBUS" paper to create scaffold fasta file.
> I extract the longest 454 scaffold fasta out. Got a file named as
> "454_reads,fasta" now.
>
> For Illumina technique read,
> Initially I got two files named as Illumina.fasta Illumina.fasta.qual
> I follow the "De-novo Solexa only assemblies" without paired-end.
> It worked perfectly by MIRA.
>
> Confusing part:
> For getting best bacteria genome assembly back by combination of  454
> technique and Illumina technique reads.
> At De-novo hybrid assemblies, All reads de-novo:
> I just throw all
> 1. Paired_end_in.454.fasta Paired_end_in.454.fasta.qual
> Paired_end_traceinfo_in.454.xml
> 2. Standard_end_in.454.fasta Standard_end_in.454.fasta.qual
> Standard_end_traceinfo_in.454.xml
> 3. Read_in.solexa.fasta Read_in.solexa.fasta.qual
> And running the command:
>
> mira --project=bchocse --job=denovo,genome,normal,454,solexa 
> >&log_assembly.txt
>
> or
>
> At De-novo hybrid assemblies, Long read first, then Solexa:
> 1. No idea how to deal with it because I not sure what is the
> hybrid_backbone_in.caf refer to?
>
> Hope anybody can help me solve this problem.
> My main purpose is using the reads from 454 technique and Illumina
> technique read to get "good" assemblies.
>
> best regards
> edge
>
>
> On Fri, Oct 16, 2009 at 8:20 AM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote:
>
>> On Freitag 16 Oktober 2009 Chia Jing Yi wrote:
>> > Refer to "Solexa sequence assembly with MIRA3", at the part of De-novo
>> > hybrid assemblies ( Solexa + ...).
>> > Can I know what is the format of input file should look like?
>>
>> Currently the default format for 454 is FASTA and for Solexa also. The
>> latter
>> may change to FASTQ in 3.0.0.
>>
>> Regards,
>>  Bastien
>>
>>
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>
>

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