Re: [galaxy-user] Megablast question

2012-04-11 Thread Jennifer Jackson 

Hi Vasu,

The three primary megablast databases available on the public main 
Galaxy instance are comprised of individual fragments/sequences of 
different types from many species (not assembled genomes):

http://user.list.galaxyproject.org/Question-about-megablast-td4543260.html

If you want to use megablast to map against specific assembled genomes, 
then using a local or (better) cloud instance is recommended. In your 
own instance, the individual genomes would be set up the way that the 
'phiX174' is set up on main.

To get started, please see: http://getgalaxy.org

Does this address your question? If not, perhaps you could explain more 
what your goal is and we can try to offer help or confirm that this is 
the best path?


Regards,

Jen
Galaxy team

On 4/10/12 11:04 AM, shamsher jagat wrote:

Hi,
I am using megablast and was wondering how can I get chromosome number
and coordinates of its hits.

Thanks

Shamesher


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[galaxy-user] Megablast question

2012-04-10 Thread shamsher jagat 
Hi,
I am using megablast and was wondering how can I get chromosome number
and coordinates of its hits.

Thanks

Shamesher
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Re: [galaxy-user] Megablast question

2012-02-16 Thread Noa Sher 

  
  
Hi Scott
I never used megablast so what i am writing is true of just any
  fasta file (so if there is anything quirky in megablast that i
  dont know about, apologies!):

  Take your fasta file and convert to tabular (under "fasta
manipulation" - this will make it go to one line per record).
  
  Then randomly choose whatever number of reads you want using
"select random lines from a file" under the text maniupulation
tab.
  Then convert the tabular file back to fasta. (under the fasta
manipulation tab)
  

noa
On 16/02/2012 19:31, Scott Tighe wrote:

  
  Hi all

When using Galaxy megablast, is there a simple way to reduce my
FASTA files from 23 million reads to 1/2 that size and submit to
megablast separately?

Thanks
  
  -- 
Scott Tighe
Advanced Genome Technology Lab
Vermont Cancer Center at the University of Vermont
149 Beaumont Avenue
Health Science Research Bd RM 305
Burlington Vermont USA 05405
lab  802-656-AGTC (2482)
cell 802-999-

  
  
  
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Re: [galaxy-user] Megablast question

2012-02-16 Thread Dannon Baker 
Noa has the right idea, but if you're asking for how to split a dataset into 
two non-overlapping halves you'll want to use Select First and Select Last, 
instead of random lines.  Get an accurate line count from your file using the 
Line/Word/Character count tool and then split it right in the middle using 
select first/last.

-Dannon

On Feb 16, 2012, at 2:35 PM, Noa Sher wrote:

 Hi Scott
 I  never used megablast so what i am writing is true of just any fasta file 
 (so if there is anything quirky in megablast that i dont know about, 
 apologies!):
   • Take your fasta file and convert to tabular (under fasta 
 manipulation - this will make it go to one line per record).
   • Then randomly choose whatever number of reads you want using select 
 random lines from a file under the text maniupulation tab.
   • Then convert the tabular file back to fasta. (under the fasta 
 manipulation tab)
 noa
 On 16/02/2012 19:31, Scott Tighe wrote:
 Hi all
 
 When using Galaxy megablast, is there a simple way to reduce my FASTA files 
 from 23 million reads to 1/2 that size and submit to megablast separately?
 
 Thanks
 -- 
 Scott Tighe
 Advanced Genome Technology Lab
 Vermont Cancer Center at the University of Vermont
 149 Beaumont Avenue
 Health Science Research Bd RM 305
 Burlington Vermont USA 05405
 lab  802-656-AGTC (2482)
 cell 802-999-
 
 
 
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 http://lists.bx.psu.edu/listinfo/galaxy-dev
 
 
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 please use the interface at:
 
   
 http://lists.bx.psu.edu/
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 at usegalaxy.org.  Please keep all replies on the list by
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