Hi all, I have 10 sets of illumina PE 250bp data.
The reads are 16S V3V4 regions.
The quality of reads drop dramatically especially in the 3'end.
I have trimmed the 3'end and merged the paired end reads using usearch7 fastq_mergepairs with 25 bp min overlap and max 1 mismatch.
Since the quality are bad and many reads are removed and some are too short to have overlapping region for merging.
But my major concern is the mismatch. I found that there are many mismatch between the forward and reverse reads in the overlapping region even I have trimmed the bad quality end. And fewer than half of the merged reads have exact match in the overlapping region.
Is it a problem?
The reads are 16S V3V4 regions.
The quality of reads drop dramatically especially in the 3'end.
I have trimmed the 3'end and merged the paired end reads using usearch7 fastq_mergepairs with 25 bp min overlap and max 1 mismatch.
Since the quality are bad and many reads are removed and some are too short to have overlapping region for merging.
But my major concern is the mismatch. I found that there are many mismatch between the forward and reverse reads in the overlapping region even I have trimmed the bad quality end. And fewer than half of the merged reads have exact match in the overlapping region.
Is it a problem?
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