User: edikedikedikedik

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Posts by edikedikedikedik

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Comment: C: Illumina HiSeq generates abnormally high duplication levels and per tile sequenc
... > I am not sure if they would be considerate enough to re-run the sample at no cost. It would depend on your relationship with them. You could always ask for a discount on a re-run. Although it would be an ideal outcome, I'm not sure either, since communication is handled by another department. ...
written 5 weeks ago by edikedikedikedik0
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Comment: C: Illumina HiSeq generates abnormally high duplication levels and per tile sequenc
... > Was this the only sample in that lane? > Do you know what the cluster density for this run was? > How much phiX was spiked in to this run? I've updated the question providing answers to these questions. Please, take a look. ...
written 5 weeks ago by edikedikedikedik0
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Comment: C: Illumina HiSeq generates abnormally high duplication levels and per tile sequenc
... Yes, we are running trimmomatic in PE mode (i.e. we trim both files simultaneously). We've reported all surviving reads (not just surviving pairs). The genome is presumably 170kbp long, and we expect ~50-70x coverage (given surviving pairs). It is enough for assembly, though it might not be sufficie ...
written 5 weeks ago by edikedikedikedik0
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Comment: C: Illumina HiSeq generates abnormally high duplication levels and per tile sequenc
... > How much data did you lose in the trimming step? I'm left with ~22% of R1 (~250k out of ~1.1mln) and ~4% of R2 reads (~41k out of ~1.1mln). ...
written 5 weeks ago by edikedikedikedik0
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Comment: C: Illumina HiSeq generates abnormally high duplication levels and per tile sequenc
... > Can you post quality score plots for R1/R2? Thank you for taking your time to respond. I've updated my post adding score plots for R1 and R2 both before and after running `trimmomatic`. ...
written 5 weeks ago by edikedikedikedik0
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Comment: C: Illumina HiSeq generates abnormally high duplication levels and per tile sequenc
... Thank you for a response. > Was this the only sample in that lane? How much > phiX was spiked in to this run? As far as we can tell there were 4 samples with largely different phage genomes. And they all exhibit these quality issues. We'll clarify if there might've been any other sample pr ...
written 5 weeks ago by edikedikedikedik0
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Illumina HiSeq generates abnormally high duplication levels and per tile sequence quality patterns in rapid-run mode
... Having received a task to assemble phage genome, I and my colleague ran into several problems. - First, the sequence duplication levels are abnormally high, reaching up to ~90% and ~40% for forward and reverse reads, respectively. ![Sequence duplication level for raw forward R1 reads][1] - Secon ...

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