Question: Picard ExtractIlluminaBarcodes: BARCODE-FILE
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gravatar for user31888
3.0 years ago by
user3188840
United States
user3188840 wrote:

Hi,

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
picard • 1.1k views
ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by user3188840
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