Re: [AMOS-help] bank-transact -c -z -b test.bnk -m test.afg exited with status: 1

[Lionel G. <guy...@gm...>]

Hi Salvador,

The quality files are generally produced by the base-calling software  
that transforms whatever raw output from the sequencer (Sanger, 454,  
Solid, ...) to bases (a fasta file, generally) and an associated  
probability for each base to be correct. Generally, sequencing  
services provide them.

One of the standard base-callers for Sanger data is Phred, and the  
quality values are often attributed the same Phred does. See http://en.wikipedia.org/wiki/Phred_quality_score 
  for details. The quality score for each base is attributed with Q =  
-10 * log(p), where p is the probability that the given base is  
correct. Thus, a score of 10 indicates an accuracy of 90%, 20 => 99%,  
30 => 99.9%, and so on. Given a chromatogram (for Sanger data), Phred  
will give you a fasta and a fasta qual file.

HTH,

Lionel



On 2 Feb 2009, at 21:02 , Salvador Ramirez wrote:

> Hi Lionel,
>
>   Thanks for your response. Unfortunetly the authors of AMOS have  
> not answered my question and also I have not been able to find  
> information about those quality files: what are they? how do you  
> normally obtain them? should they come from the sequencing service?
>
> Thanks in advance.
>
> ---sram
>
> Lionel Guy wrote:
>> Hi Salvador,
>> I guess you can generate fake quality scores for your reads,  
>> although this might really affect the way the assembler works.
>> Given that your seq file is like this:
>> >read1
>> ACGTGTG
>> >read2
>> GGCTGCT
>> you could have a qual file like this:
>> >read1
>> 30 30 30 30 30 30 30
>> >read2
>> 30 30 30 30 30 30 30
>> Alternatively, you may try to experiment with the -gq and -bq  
>> options, but I don't know if they actually replace a qual file. For  
>> more info, see:
>> http://amos.sourceforge.net/docs/converters/toAmos.html
>> You may also try the other converter tarchive2amos and its -qual  
>> option:
>> http://amos.sourceforge.net/docs/converters/tarchive2amos.html
>> The authors of AMOS might have some smarter suggestions...
>> Cheers,
>> Lionel
>> On 1 Feb 2009, at 1:29 , Salvador Ramirez wrote:
>>> Hi Lionel,
>>>
>>> Thanks for your response. Actually I don't have quality scores for  
>>> my reads. What should I do if I just have the fasta file with reads?
>>>
>>> Thanks,
>>>
>>> ---sram
>>>
>>> Lionel Guy escribió:
>>>> Hi Salvador,
>>>>
>>>> Do you have any quality scores associated with your reads? You  
>>>> will need a fasta qual file (option -q in toAmos) to use bank- 
>>>> transact:
>>>>
>>>> toAmos -s test.seq -q test.qual -o test.afg
>>>>
>>>> I'm not sure you can have it working without quality data.
>>>>
>>>> HTH,
>>>>
>>>> Lionel
>>>>
>>>> On 30 Jan 2009, at 17:17 , Salvador Ramirez wrote:
>>>>
>>>>> Dear people,
>>>>>
>>>>>   I recently downloaded amos because I need to use
>>>>> AMOScmp-shortReads. I followed instructions at
>>>>> http://www.cbcb.umd.edu/research/SR-assembly-tutorial.shtml but  
>>>>> I get an
>>>>> error. Basically what I did is the following:
>>>>>
>>>>> 1.- To create a file called test.seq with all my reads on fasta  
>>>>> format.
>>>>> 2.- To create a file with my reference genome. In particular one
>>>>> chromosome fasta sequence which I renamed as test.1con
>>>>> 3.- toAmos -s test.seq -o test.afg
>>>>> 4.-AMOScmp-shortReads test
>>>>>
>>>>> entonces el programa se ejecuta pero arroja el mensaje de error:
>>>>>
>>>>> bank-transact -c -z -b test.bnk -m test.afg exited with status: 1
>>>>>
>>>>> Also, in the test.runAmos.log first appeared a lot of errors:
>>>>> ---------------------
>>>>> START DATE: Fri Jan 30 08:27:15 2009
>>>>> Bank is: test.bnk
>>>>>  0%                                            100%
>>>>> AFG ERROR: Sequence and quality lengths disagree
>>>>> could not parse 'RED' message with iid:1, message ignored
>>>>> ERROR: Sequence and quality lengths disagree
>>>>> could not parse 'RED' message with iid:2, message ignored
>>>>> ERROR: Sequence and quality lengths disagree
>>>>> could not parse 'RED' message with iid:3, message ignored
>>>>> -------------------
>>>>>
>>>>> and finally the previously mentioned error.
>>>>> I wonder if I am doing something wrong.
>>>>>
>>>>> Thanks for your time.
>>>>> Best,
>>>>>
>>>>> ---sram
>>>>
>>>
>> ============================================
>> Lionel Guy
>> Thunmansgatan 25, SE-75421 Uppsala
>> phone: +46 (0)18 245596
>> mobile: +46 (0)73 9760618
>> email: guy...@gm...
>> ============================================

============================================
Lionel Guy
Thunmansgatan 25, SE-75421 Uppsala

phone: +46 (0)18 245596
mobile: +46 (0)73 9760618
email: guy...@gm...
============================================