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Old 05-05-2016, 06:53 AM   #11
rEDI
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Location: United Kingdom

Join Date: Apr 2016
Posts: 14
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Thanks Genomax and Fanli

I recently read a paper that sequenced 96 samples of fish gut on MiSeq, with V4 primer set, the exact same as mine.

That study obtained ~3m reads in total after QC. Therefore approx 32k reads/sample.

I only sequenced 24, therefore obtaining the higher number of reads per sample.

Looking at my reads, had I sequenced 96 samples, I would have received comparable numbers to the other study (~approx. 25k/sample).

The read assembly is fine, just high numbers of reads per sample.

Am I right in saying this is due to low number of samples multiplexed (24), and that I can just rarefy to the lowest number of QC'd and assigned reads (150k in one experiment, 300k in another)??

What do you think?

Thank you

Last edited by rEDI; 05-05-2016 at 07:05 AM.
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