[mira_talk] Re: * in padded file?
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 13 May 2011 12:03:16 +0200
A 2-sec google search for "padded unpadded sequence" got me that result from
the mira mailing list:
//www.freelists.org/post/mira_talk/Convert-project-problem,1
And the well-written, comprehensive documentation is here:
http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html
Lionel
On 13 May 2011, at 11:58 , Peter wrote:
> On Fri, May 13, 2011 at 9:43 AM, Shabhonam Caim (TGAC)
> <Shabhonam.Caim@xxxxxxxxxxx> wrote:
>>
>>
>> Hi All,
>>
>> Few basic beginner’s questions:
>>
>> 1. Can anyone please tell me, what are the * character in padded file
>> and how is it going to affect the alignment. Do we consider the padded file
>> or the unpadded file?
>
> You probably want to work with the unpadded file (which has no * characters).
>
> The padded file contains * characters representing gaps supported by at
> least one read. This makes sense if you are familiar with the ACE file format,
> which uses this convention. You'll see the same gapped sequence in the
> ACE file from MIRA, and this can be viewed in an assembly viewer.
>
>> 2. The best way to assemble a transcriptome data?
>>
>> I have used the following command to assemble the 454 reads:
>>
>> mira-3.0.0 mira --project=test --job=denovo,genome,draft,454 454_SETTINGS
>> -LR:mxti=no -FN:fai=all_454_female_male.fna -FN:fqui=male_female.qual
>>
>> but later I realized that it was a transcriptome data, can anyone help me
>> out in changing the parameters so that I can assemble the transcrpitome
>> data.
>
> The main thing is the job parameter changes from genome to est. You
> have looked at the documentation, haven't you? ;)
>
> Peter
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