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Old 01-27-2015, 10:14 AM   #8
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Originally Posted by Marisa_Miller View Post
Hi Brian,

Does the subsampling tool randomly subsample reads? The program I am using now (Geneious) only takes the first specified % of reads and does not randomize.

Thank you,
Yes, it randomly subsamples. You can set the RNG seed with "sampleseed=NUMBER" if you want deterministic random sampling; by default, the seed is random.

Reformat can also give the first X reads with the "reads=X" flag, or combine the reads=X and samplerate=Y to subsample a fraction of the first X reads, etc.
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