I have a MiSeq run which produced two fastq files; one of which contained all forward reads, and the second all reads in the same orientation that needed to be reverse complimented.
In my data each fastq file shows a mixture of orientated reads:
I guess that make_contigs script designed to join overlapping PE reads will not be able to take into consideration the mixture of Fwd and Rev sequences in each file?
is this normal, or should I be seeing all Fwd and Rev primer sequences in separate Fastqs?
is there any way to analyses such data by MOTHUR?
I also have barcode with variable length?
I have used mothur for 454 data analysis but i a new to Illumina data and not good in custom scripting.
Any help for demultiplexing of such a complex data would be really great.