I have paired end reads of Miseq 2x300 of region V3 and V4 of 16S.
My reads had a forward of V3 and reverse of V4
primer CCTACGGGIGGCWGCAG GACTACHVGGGTATCTAATCC
barcode TAAGGCGA TAGATCGC POF.4.0
barcode TAAGGCGA CTCTCTAT OF.9.0
barcode TAAGGCGA TATCCTCT POF.4S.0
barcode CGTACTAG TAGATCGC OF.9S.0
barcode CGTACTAG CTCTCTAT OF.7.1
barcode CGTACTAG TATCCTCT OF.9.1
barcode AGGCAGAA TAGATCGC POF.4S.1
barcode AGGCAGAA CTCTCTAT OF.9S.1
barcode AGGCAGAA AGAGTAGA OF.7.2
barcode TCCTGAGC AGAGTAGA OF.9.2
barcode TCCTGAGC GTAAGGAG OF.7S.2
barcode TCCTGAGC ACTGCATA POF.5S.3
barcode GGACTCCT ACTGCATA POF.4.4
barcode GGACTCCT AAGGAGTA OF.7.4
barcode GGACTCCT CTAAGCCT OF.7S.4
barcode TAGGCATG GTAAGGAG OF.7.5
barcode TAGGCATG AAGGAGTA OF.7S.5
When I run the make.contigs command:
make.contigs (ffastq=R1.fastq.gz, rfastq=R2.fastq.gz, oligos=map)
I get 298178 seqs, but in each fastq.gz (1-2) I have 52000 and 64000 reads respectively, then the final contigs must be 52000 contigs or seqs (one read of R1 with one read of R2). Also in the report, I have overlaps of 4, 36, 1, bases, but in accord with my library the overlap must be of 150 bases aprox. I want to know what happen with make.contigs, why I have more contigs than reads?
Thank you so much.