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Old 05-26-2019, 10:04 PM   #1
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Join Date: May 2019
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Question bcl2fastq fail to demultiplexing, Barcode collision

bcl2fastq --barcode-mismatches 1 -o ./test --tiles s_6 --sample-sheet SampleSheet_L006_8index.csv

2019-05-27 13:33:58 [28b0880] ERROR: bcl2fastq::common::Exception: 2019-May-27 13:33:58: Success (0): /TeamCityBuildAgent/work/556afd631a5b66d8/src/cxx/lib/layout/BarcodeCollisionDetector.cpp(187): Throw in function void bcl2fastq::layout::BarcodeCollisionDetector::handleCollision(const value_type&, const value_type&)
Dynamic exception type: boost::exception_detail::clone_impl<bcl2fastq::layout::BarcodeCollisionError>
std::exception::what: Barcode collision for barcodes: GACCTGAT, CAGCTGAT
By default, bcl2fastq allows 1 mismatch in each barcode. Barcodes with too few mismatches are ambiguous ( less than 2 times the number of mismatches plus 1). To reduce the number of allowed mismatches, use the command line option: '--barcode-mismatches'. Note that particularly for barcodes with only 1 mismatch, there is the danger that some reads will be written to the wrong sample due to errors in the barcode sequence.

What's wrong about bcl2fastq ? index GACCTGAT, CAGCTGAT have two base different, I cannot see collision between GACCTGAT, CAGCTGAT.
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