Dear Galaxy-users,

Does anyone know what the differences are between hg19 and hg19patch2 and can 
anyone tell me if the latest ensembl gtf file (v62) is definitely compatible 
with both hg19 and hg19patch2?


Best Wishes,
David.

__________________________________
Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.

Tel. +44 117 3312058
Fax. +44 117 3312091

d.a.matth...@bristol.ac.uk






On 10 Jun 2011, at 11:39, Michal Stuglik wrote:

> 
> 
> Hi Jen,
> 
> It works, thanks! 
> 
> I am wondering why using Text Manipulation/Compute function, galaxy changes 
> brackets '[' to '__ob__' and '__cb__' for ']', so for this: str(c1)[1:2] --> 
> str(c1)__ob__1:2__cb__  
> 
> thanks a lot,
> michal
> 
>> Hi Michal, 
>> 
>> The tool "Fetch Sequences -> Extract Genomic DNA" can be used to extract 
>> fasta sequences. The coordinates can be BED, GTF, etc. and the "genome" 
>> doesn't necessarily have to be an actual genome, just a fasta file in your 
>> history. 
>> 
>> To subset a data string, the tool "Text Manipulation -> Trim" might be 
>> helpful. This would only work if you want to use the same rules for an 
>> entire file (or split your file up and run the tool on those subfiles using 
>> different rules). Practical for some cases, but not all. 
>> 
>> And the final option is for coordinate data - tools in "Operate on Genomic 
>> Intervals". Once you have the final coordinate set, going back and using the 
>> "Fetch Sequences" tool can capture the associated result fasta sequence, 
>> from a native genome or a fasta file in your history, as described above. 
>> 
>> Hopefully this gives you an option that will work for your project, 
>> 
>> Best, 
>> 
>> Jen 
>> Galaxy team 
>> 
>> On 6/5/11 7:14 AM, Michal Stuglik wrote: 
>>> 
>>> Hi all, 
>>> 
>>> I am wondering if galaxy has tool to substring/extract sequence/text 
>>> from another sequence/text based on coordinates in columns (start, end 
>>> column) or how to do it in Text Manipulation/Compute? 
>>> 
>>> all the best, 
>>> michal 
>>> 
> 
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___________________________________________________________
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