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 802-999-6666

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