[mira_talk] Re: bad assembly and scaffolding
- From: Martin Mokrejs <mmokrejs@xxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 06 Nov 2010 16:27:08 +0100
Bastien Chevreux wrote:
> On Donnerstag 04 November 2010 Enrico Lavezzo wrote:
>> I am trying to use Mira (and Bambus) in order to perform an assembly of a
>> bacterial genome. I am following the pdf guide (supplied in the
>> documentation) for the various steps and commands, but I am obtaining some
>> poor results and I am wondering whether I am doing something wrong. Here
>> are the commands I used, could you please let me know if there are
>> mistakes?
>>
>> Mira:
>>
>> sff_extract -o output fileShotGun.sff
>> sff_extract-o Ecoli -a -l linker -i "insertsize:7810,insert_stdev:1532"
>> FilePairedEnds.sff
>> mira--project=output --job=denovo,genome,accurate,454
>
> Hello Enrico,
>
> it's almost right. I had to look at it twice to find the problem. You have
>
> sff_extract ... -i "insertsize:7810,insert_stdev:1532"
>
> while it must be
>
> sff_extract ... -i "insert_size:7810,insert_stdev:1532"
>
> Mind the additional "_" in "insert_size".
BTW, why doesn't mira die on unexpected attributes? Is there no way to check
the user input for supported tags? Or why doesn't it at least Warn the user
something was not interpreted and kept just as some "user-provided comment"?
;-)
Martin
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