Discarding duplicate reads from fastq file on the basis of random barcode

Question

[naeem40thju]

Say, I have used an oligo containing random barcode (Ns) for excluding the duplicated reads (PCR biased reads) Oligo: CCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNNNNNNTGTAAAACGACGGCCAGT

So, how can I exclude/remove the duplicated reads from the fastq file? Thanks.

[GenoMax]

Where is this sequence supposed to appear in your reads? How is this sequence going to identify duplicate reads?

BTW: You have already received answers to do this in your last question here: How can I extract the sequencing reads containing a specific linker/tag?

Please don't post the same question in multiple threads.