I'm looking for a convenient tool, to demultiplex my Illumina PE data. Particularly to extract pairs with a certain sequence in the forward read and other certain sequence in the reverse one. Could you advise me please? For example: Initially, we have two fastq files with forward and reverse reads
Forvard reads sequences:
NNNNNNAGTCCGTATATGCCGAGNNNNNNNN NNNNNNAGAGCGTATATGCCGAGNNNNNNNN NNNNNNAGTCCGTATATGGGGAGNNNNNNNN
Reverse reads sequences:
NNNNNNNNNGAGATGGACTACTCACNNNNNN NNNNNNNNNGAGATGGATTACTCACNNNNNN NNNNNNNNNGAGAAGGACTACTCACNNNNNN
So, i'd like to extract for futher analysis only pair
Since in the forward read is AGTCCGTATATGCCGAG tag and there is GAGATGGACTACTCAC tag in the reverse read. Now i need only 100% match.