I don't understand what is the barcode file to be used with Picard ExtractIlluminaBarcodes. Picard user guide (here) mentions that we have to provide a BARCODE_FILE:
"Tab-delimited file of barcode sequences, barcode name and, optionally, library name. Barcodes must be unique and all the same length. Column headers must be 'barcode_sequence_1', 'barcode_sequence_2' (optional), 'barcode_name', and 'library_name'."
Are these barcodes the indexes used during the library prep (e.g. AD002, AD005, ...)?
My RunInfo.xml file looks like this:
<Reads> <Read NumCycles="76" Number="1" IsIndexedRead="N" /> <Read NumCycles="6" Number="2" IsIndexedRead="Y" /> <Read NumCycles="76" Number="3" IsIndexedRead="N" /> </Reads>
My READ_STRUCTURE is thus: 76T6B76T
But what about the BARCODE_FILE? How it should look like? Something like the following maybe?
barcode_sequence_1 barcode_name library_name AD002 CGATGT Library_1 AD005 ACAGTG Library_1 AD006 GCCAAT Library_1