Hello HiSeq2000 users,
we just finished a multiplexed mRNA-seq run on the HiSeq2000 with puzzling results, maybe somebody encountered this phenomenon before:
We prepared 6 mRNA-seq libraries using the illumina TruSeq kit incl. the indexed RNA adapters and sequenced using a 50x cycle single-end run on the HiSeq 2000 on a single lane. The insert cycles (1-50) yielded sequences of reasonable quality, although the cluster density on that lane was pretty high (around 1'000 clusters/mm^2). From cycles 51-58 (the index/barcode) we do not get any sequence information (NNNNNNNN), which means the do-convolution of the samples failed. On the same flow cell there was another multiplexed sample, using the same indexing system (illumina TruSeq) and this worked out pretty fine.
Any idea, what went wrong here???
we just finished a multiplexed mRNA-seq run on the HiSeq2000 with puzzling results, maybe somebody encountered this phenomenon before:
We prepared 6 mRNA-seq libraries using the illumina TruSeq kit incl. the indexed RNA adapters and sequenced using a 50x cycle single-end run on the HiSeq 2000 on a single lane. The insert cycles (1-50) yielded sequences of reasonable quality, although the cluster density on that lane was pretty high (around 1'000 clusters/mm^2). From cycles 51-58 (the index/barcode) we do not get any sequence information (NNNNNNNN), which means the do-convolution of the samples failed. On the same flow cell there was another multiplexed sample, using the same indexing system (illumina TruSeq) and this worked out pretty fine.
Any idea, what went wrong here???
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