[mira_talk] Re: 454 fasta files

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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