[mira_talk] Re: Fishy tag
- From: Louis Letourneau <louis.letourneau@xxxxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 16 Feb 2011 16:06:56 -0500
yeah, that works fine.
I just wanted to play with the other tools that come downstream from
using the genbank file.
Louis
On 11-02-16 04:05 PM, John Nash wrote:
> Have you tried with the FASTA file instead of the GBF one?
>
> J
>
>
> On 2011-02-16, at 4:03 PM, Louis Letourneau wrote:
>
>> I just tried 3.2.1.5 and got the same result.
>> The length is right there though, and I haven't manipulated the file in
>> any way.
>> --->
>> Loading backbone from GBF file: staphAureus_backbone_in.gbf
>>
>> Fishy tag (to is greater than sequence length of 0):
>> --->
>>
>> $ head staphAureus_backbone_in.gbf
>> LOCUS NC_007793 2872769 bp DNA circular BCT
>> 13-MAY-2010
>> DEFINITION Staphylococcus aureus subsp. aureus USA300_FPR3757, complete
>>
>>
>> $ mira --version
>> This is MIRA V3.2.1.5 (development version).
>>
>> Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
>> Assembly Using Trace Signals and Additional Sequence Information.
>> Computer Science and Biology: Proceedings of the German Conference on
>> Bioinformatics (GCB) 99, pp. 45-56.
>>
>>
>>
>> Is the length read from LOCUS line?
>>
>> Louis
>>
>> On 11-02-16 03:53 PM, Bastien Chevreux wrote:
>>> On Wednesday 16 February 2011 21:46:35 Bastien Chevreux wrote:
>>>> You have two options:
>>>> 1) try out a current development version of MIRA (3.2.1.5), where this bug
>>>> is fixed. For that, head to
>>>> http://sourceforge.net/projects/mira-assembler/files/MIRA/development/
>>>> 2) convert the DOS format of the GenBank file to Unix format. I'd use
>>>> dos2unix or a number of other available tools for this.
>>>> http://kb.iu.edu/data/acux.html
>>>> gives a good overview
>>>
>>> On a second thought ... in case you have much more than 10m reads, going
>>> with
>>> 3.2.1.5 might be a better choice if you do not want to wait for too long
>>> for
>>> the assembly to finish.
>>>
>>> B.
>>>
>>
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>
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