I have a target PCR basic custom library with a unique initial barcode (IonTorrent barcode). For example, I amplified two regions... the two regions start with a common sequence "linker" and then they have a "region barcode", like
AAAAAAAAnBBBBBBBnnnnnnnnnn (first_region:AAA...=linker, BBB...=region1_barcode,n=nucleotide) AAAAAAAAnCCCCCCCnnnnnnnnnnn (second_region:AAA...= linker, CCC...=region2_barcode,n=nucleotide)
Is there any tool that can help me to split the reads in two fastq, by region barcode? I want to do this before to map with BWA. For multimapping reasons I can not map all reads in a fasta with the two conting or all reads in each single contig fasta.
In the ReadGroup is not reported any barcode and I do not want to use something like "grep" or similar because in my region_barcode (BBB... CCC...) I could have a mismatch due to PCR/sequencig error.