Is the default parameter setting too harsh for 16S V4

[mingjiew]

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I have MiSeq sequencing data (150bp x 2) for the V4 (~250bp) region. Is the default parameter setting for read merging too harsh?

[jstjohn]

Quite possibly. I would for sure play around with parameters. When I wrote this years ago 150bp paired end data was not a common occurrence.

On September 28, 2016 at 2:08:01 PM, mingjiew ([email protected]) wrote:

I have MiSeq sequencing data (150bp x 2) for the V4 (~250bp) region. Is the default parameter setting for read merging too harsh?

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