Hi Tim,
Great thanks - yeah my old buddy read structure was the culprit as I missed
the 8B like you mention.
Thanks
K
On Monday, June 16, 2014, Tim Fennell <tfenn...@broadinstitute.org> wrote:
> Hi Kristian,
>
> Your read_structure parameter tells ExtractIlluminaBarcodes to do exactly
> what you're suspecting. 101T8B101T states that there is only one barcode
> read. Perhaps it should be 101T8B8B101T?
>
> -t
>
> On Jun 15, 2014, at 6:31 PM, Kristian Andersen <kga1...@gmail.com
> <javascript:_e(%7B%7D,'cvml','kga1...@gmail.com');>> wrote:
>
> Hi All,
>
> I have run into the following problem that I was hoping somebody could
> help me with.
>
> I have been trying to demultiplex some Illumina (101bp PE, dual barcoded)
> libraries using Picard - e.g.:
>
> java -Xmx2g -jar
> /seq/software/picard/1.626/bin/ExtractIlluminaBarcodes.jar
> BASECALLS_DIR=/analysis/140615/_temp/140615.H9FT9ADXX/Data/Intensities/BaseCalls/
> LANE=2 READ_STRUCTURE=101T8B101T
> BARCODE_FILE=/analysis/140615/barcodeData.2
> METRICS_FILE=/analysis/140615/_logs/barcode.metrics.H9FT9ADXX.2.txt
> MAX_MISMATCHES=0 MINIMUM_BASE_QUALITY=25 NUM_PROCESSORS=1
>
> I have done this a million times before, but with these new libraries I
> keep getting the following error messages:
>
> Barcode AGGCAGAA specified more than once in /analysis/140615/barcodeData.2
> Barcode CAGAGAGG specified more than once in /analysis/140615/barcodeData.2
> Barcode CAGAGAGG specified more than once in /analysis/140615/barcodeData.2
> .
> .
> .
>
> I have never seen this happen before and I have tried everything (I can
> think of...) to fix the problem. Basically it appears as if Picard isn't
> accepting the dual barcodes and just treats them individually - which is
> strange, since I have demultiplexed many runs that were dual barcoded. If I
> just to try to demultiplex samples where both barcodes are different, then
> everything goes through.
>
> My barcode data files look like this:
> barcode_name library_name barcode_sequence_1 barcode_sequence_2
> H9FT9ADXX-EM-096_NuGEN EM-096_NuGEN AGGCAGAA TATCCTCT
> H9FT9ADXX-EM-098_NuGEN EM-098_NuGEN AGGCAGAA AGAGTAGA
> H9FT9ADXX-EM-095B_NuGEN EM-095B_NuGEN CAGAGAGG TAGATCGC
> H9FT9ADXX-G3691-1_NuGEN G3691-1_NuGEN CAGAGAGG CTCTCTAT
> H9FT9ADXX-K562B_NuGEN K562B_NuGEN CAGAGAGG CTAAGCCT
> H9FT9ADXX-EM-095_NuGEN EM-095_NuGEN CTCTCTAC CTAAGCCT
> H9FT9ADXX-G3670-1_NuGEN G3670-1_NuGEN CTCTCTAC TAGATCGC
> H9FT9ADXX-G3679-1_NuGEN G3679-1_NuGEN CTCTCTAC TATCCTCT
> H9FT9ADXX-G3680-1_NuGEN G3680-1_NuGEN CTCTCTAC
>
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Find What Matters Most in Your Big Data with HPCC Systems
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Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems
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