<p>Dear all,</p>

<p>I have some questions regarding demultiplexing Illumina BCL files. First question is if Illumina&acute;s Undetermined Fastq files contains barcodes?</p>

<p>Second question - If I would like to provide demultiplexing and keep my barcodes in fastq files (no in the header like CASAVA provide, but inside the read sequence) - does anybody have any experience how to do that?</p>

<p>Thak you for any sharing your experience.</p>

<p>Yes, the undetermined files have the barcodes in the header of each read.</p>

<p>I haven&#39;t a clue how you would include read #2 into read #1, though perhaps playing with --use-bases-mask would do the trick (presumably by adding the index length to that of read1). It would make more sense to me to just write read 2 as separate file (so paired end experiments will have all three reads rather than just two).</p>
