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Old 05-05-2016, 12:46 AM   #4
rEDI
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Location: United Kingdom

Join Date: Apr 2016
Posts: 14
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Hi Fanli

Do you think that rarefying my data to 300k seqs/sample is also ok, or too deep?

In one run I obtained slightly more reads passing filter, and so I rarefied to that sample containing the the lowest no of reads (apprx. 300k).

Some studies use much lower no. of reads, whilst others use numbers comparable to mine. I suppose it also depends on the number of samples sequenced (i.e. 24 samples will produce more seqs passing filter than 96 samples)?

Please let me know what you think.

Kind regards
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