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Old 04-21-2016, 12:40 AM   #1
Location: United Kingdom

Join Date: Apr 2016
Posts: 14
Default Sequencing depth

I am sequencing samples from animal gut using illumina MiSeq/HiSeq, targeting the v4 region of the 16S

I get 22m raw reads back from MiSeq (after removal of PhiX etc), for a total of 24 samples.

I am getting an average of ~400,000 classified reads per sample after filter steps have been performed in Mothur.

I then rarefy to the sample with lowest no of reads (approx 150k seqs).

The rarefaction curves plateau after approx 60k reads or so.

Do you think the sequencing is too deep, and if so is this a big problem?

Thank you
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