I recently ran a NextSeq 2000 using 6-nucleotide Illumina TruSeq unique indices. My goal is to demultiplex using bcl2fastq and extract only the reads that match my indices. However, there's a complication: the run included samples from another person whose 8-nucleotide R1 indices overlap with my indices.
I'm looking for advice on:
How can I effectively run the bcl2fastq tool to extract only the reads that exhibit a precise match with my own 6-nucleotide indices?
Is it possible to execute the demultiplexing process while concurrently generating distinct fastq files for the indices? This would let me match index entries to reads in the sample fastq files, enabling removal based on the index fastq file.
Any insights on these methods would be appreciated. Thank you.