[mira_talk] Re: 454 fasta files

Hello Bastien,   Thanks. That is very helpful.


Cheers,
Wen


On Wed, Jun 17, 2009 at 4:25 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:

> On Mittwoch 17 Juni 2009 Coffee Bean wrote:
> > [...]
> > However, all I have are the 454
> > reads are in fasta format and if I use the fasta formated 454 reads, what
> > should I do to indicate these fasta input files are from 454 (not from
> > other technologies) on the command line?
>
> Hello Wen,
>
> there are a number of ways to do this, but the most straightforward one
> probably is to use the "--job" switch.
>
> Assuming you have named your input files (FASTA and FASTA quality files):
>
>   myproject_in.454.fasta
>   myproject_in.454.fasta.qual
>
> then all you need is (if this is for a de-novo genome assembly):
>
>  mira --project=myproject --job=denovo,genome,accurate,454 --notraceinfo
>
> Please note that the "--notraceinfo" is there only because you didn't write
> anything about ancillary data in XML files. In that case, you must make
> sure
> that your data in the FASTAs is already well clipped (and is not the native
> 454 paired-end format etc.pp).
>
> Which brings me to
>
> > I read the README_454 and found out that MIRA2 only accept 454 .sff
> > files as input files, unless I misread it.
>
> Actually, MIRA does not read SFF at all.
>
> But I like it when users come with SFF instead of FASTAs. That's because
> there's a script "sff_extract" written by Jose Blanca (I can't thank him
> enough
> for that) which extracts all needed information from the SFF files
> (sequence,
> qualities, clippings, even rework paired-end data) and creates files which
> can
> be immediately used by MIRA and where no problem should be expected.
>
> > I understand that someone may have raised this question before but I
> > couldn't find the question on the archives in MIRA_talk. If anyone could
> > help me, please? I really appreciate it.
>
> I would like to urge you to read the walk-through for 454 data which is
> delivered with MIRA. It is located in "docs/html/mira_454dev.html"
>
> Hope it helps :-)
>
> Bastien
>
>
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