Hi guys,
I'm new to this forum and have a question I couldn't find an answer to.
I plan to sequence fish fin samples to investigate mucosal microbiota. I already run a pilot study with 454 but due to cost issues I want to change to MiSeq.
With 454 I sequenced the V1-V2 region of the 16S and got nice results. For MiSeq most publications present results of V4 sequencing (e.g. Kozich et al 2013). I already asked P. Schloss (mothur) for his opinion and he recommended to use V4 since V1-2 is longer than 250 bp and thus the two reads wouldn't fully overlap what would lead to higher error rates and poor quality data.
In my institute another group develops a protocol for V1-2 for MiSeq to compare their existing results with Roche 454 to the new ones and there it makes sense to use the same region of the !6S, then.
Apart from that I couldn't find a satisfying explanations and would be very happy if you have one.
So, what are the advantages/disadvantages to use V1-2 or V4 of the 16S to sequence on MiSeq?
Thanks in advance!
fish
I'm new to this forum and have a question I couldn't find an answer to.
I plan to sequence fish fin samples to investigate mucosal microbiota. I already run a pilot study with 454 but due to cost issues I want to change to MiSeq.
With 454 I sequenced the V1-V2 region of the 16S and got nice results. For MiSeq most publications present results of V4 sequencing (e.g. Kozich et al 2013). I already asked P. Schloss (mothur) for his opinion and he recommended to use V4 since V1-2 is longer than 250 bp and thus the two reads wouldn't fully overlap what would lead to higher error rates and poor quality data.
In my institute another group develops a protocol for V1-2 for MiSeq to compare their existing results with Roche 454 to the new ones and there it makes sense to use the same region of the !6S, then.
Apart from that I couldn't find a satisfying explanations and would be very happy if you have one.
So, what are the advantages/disadvantages to use V1-2 or V4 of the 16S to sequence on MiSeq?
Thanks in advance!
fish
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