Thank you very much Jeremy.

Can I have a look at the re-ran datasets?


On Thu, Oct 13, 2011 at 12:12 PM, Jeremy Goecks <jeremy.goe...@emory.edu>wrote:

> Chandu,
>
> There are two problems:
>
> (1) you mapped your reads to AgamP3, but the dbkeys for all of your
> Cufflinks datasets is anoGam1. This should not have happened automatically
> with Galaxy, but I'm looking into the issue now. Did you do this yourself?
>
> (2) Galaxy does not have sequence data for anoGam1, and this directly led
> to the problem that you're seeing.
>
> I corrected the problem by manually assigning build AgamP3 to your
> Cufflinks datasets and then rerunning Cuffcompare. In the future, I expect
> that we'll add anoGam1 data to our public server, but it's not clear when
> this will occur.
>
> Thanks,
> J.
>
>
>
> On Oct 12, 2011, at 5:35 PM, Chandu Galaxy wrote:
>
> Thank you Jeremy. I've shared my History named 'Mosquito Work: RNA-Seq
> analysis 2' with you just now. Please see the datasets from 1-58 (also see
> deleted datasets). Thanks.
>
> --
> Chandu
>
> On Wed, Oct 12, 2011 at 2:02 PM, Jeremy Goecks <jeremy.goe...@emory.edu>wrote:
>
>> Chandu,
>>
>> Are you running your analysis on our public server ( main.g2.bx.psu.edu)? If 
>> so, can you share your history me please
>> (Options-->Share/Publish-->Share with a User-->my email address).
>>
>> Thanks,
>> J.
>>
>> On Oct 11, 2011, at 4:26 PM, Chandu Galaxy wrote:
>>
>> Thank you for the response.
>> I can't check my reference genome dataset because I'm using reference
>> provided by Galaxy (*Mosquito (Anopheles gambiae): AgamP3*). Is there any
>> solution? Thank you.
>>
>> --
>> Chandu
>>
>>
>>
>> On Mon, Oct 10, 2011 at 7:15 AM, Jeremy Goecks 
>> <jeremy.goe...@emory.edu>wrote:
>>
>>>
>>> Tool execution generated the following error message:
>>>
>>> Error running cuffcompare. Warning: Your version of Cufflinks is not 
>>> up-to-date. It is recommended that you upgrade to Cufflinks v1.1.0 to 
>>> benefit from the most recent features and bug fixes 
>>> (http://cufflinks.cbcb.umd.edu).
>>> No fasta index found for ./input1. Rebuilding, please wait..
>>> Error: sequence lines in a FASTA record must have the same length!
>>>
>>> Chandu,
>>>
>>> Cufflinks/compare/diff requires that your reference genome dataset have
>>> the following format:
>>>
>>> >my_chrom
>>> AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT
>>> AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT
>>> AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT
>>> ...
>>>
>>> Note that all lines of sequence data have the same length.
>>>
>>> The problem you're seeing is because there are lines in your sequence
>>> data that are not the same length, e.g.
>>>
>>> >my_chrom
>>> AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGT
>>> AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTA
>>> AGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCGGTAGTTACCG
>>> ...
>>>
>>> The FASTA Width tool in Galaxy can help you format your dataset
>>> correctly.
>>>
>>> Good luck,
>>> J.
>>>
>>
>>
>>
>
>
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