I ran a MiSeq with v3 kit, the run was complete with cluster density 1788, but no cluster pass filter and data, the error message showed no FASQ file was generated. Is there anyone has an idea what is going on?
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The cluster density is crazy high. I'm not surprised that nothing passed filter! Can you provide some details on what kind of library it was and how much you loaded onto the flow cell? -
None of the clusters passed filter because this run was overloaded (which likely led to problems with cluster identification/purity). You may be able to recover some data (but it may have a lot of N's etc) by manually processing the raw data with bcl2fastq/blc2fastq2 and choosing the option "include failed" reads. I don't know if this is possible to do with MiSeq reporter on the MiSeq itself.
Don't have much hope of recovering useful data out of this run.Comment
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Nextera library at 15 pM
How much should the cluster density be for MiSeq?Comment
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For a regular (not low-diversity) run and V3 reagents, I'd aim for ~1,100K/mm^2. Illumina claims you can go higher than that, but I try not to push the envelope since we're a core facility, and I'm spending other people's money.
Unfortunately, my experience has been the getting optimal cluster density is very library dependent. That said, because we're a core facility, we run a lot of different libraries. I've only ever had to go up above 10 pM once to get good cluster density and that was with a TruSeq RNA library that I had to load at 20 pM.Comment
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thanks. I'll re-run the experiment with lower input.Comment
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