Hi all,
I am new to 16S metagenomics,
now I have a batch of 16S illumina PE 250bp reads generated from 10 samples.
The reads target on V3 V4 region of 16S and around 440bp after merging the forward and reverse reads.
I have quality trimmed and merged the paired end reads,
I am now not sure whether I should dereplicate the reads before removing chimeric reads and map to greengenes 97% otu.
some said remove identical reads is needed due to artificial replicates.
Any advise on dereplicate issue?
I wonder if dereplication would alter the abundance counting on each otu?
Thanks!
I am new to 16S metagenomics,
now I have a batch of 16S illumina PE 250bp reads generated from 10 samples.
The reads target on V3 V4 region of 16S and around 440bp after merging the forward and reverse reads.
I have quality trimmed and merged the paired end reads,
I am now not sure whether I should dereplicate the reads before removing chimeric reads and map to greengenes 97% otu.
some said remove identical reads is needed due to artificial replicates.
Any advise on dereplicate issue?
I wonder if dereplication would alter the abundance counting on each otu?
Thanks!
Comment