I did get the first data from a 2x260 bp run of genomic DNA. The quality of the second read was not this great - beginning from the first bases. I was lucky that my library had an average insert size of only 450 b - thus there was a huge overlap. Ea-utils fastq-join was able to merge 61% of the reads. This run generated 2x16 million reads.
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16.5 M PF pairs is on the high end of what you should expect. (That's at 1000 cluster density with 89% PF).Originally posted by james hadfield View PostComment
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We did complete the first run for a 2 x 250 bp multiplex sample. It took ~36 h for the run to complete. The library used for this run was known to be not "normal" so I am not going to comment on the data quality.Comment
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A few pictures regarding v2 quality are attached from our phiX control run (2x250bp). However, when we tried to use our inhouse amplicon products, we got quite ugly results...Last edited by Vinz; 09-17-2012, 05:49 AM.Comment
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These are some pictures showing the quality of our first run (2x250 bp and 2 indices) where we tried to do amplicon sequencing. The same library had been run with the 300 kit successfully giving nice reads and good Q values.
I was told there was not enough diversity. We will give it a try and spike in more phiX. But I am not sure this is the only problem. The constructs are based on the published TrueSeq sequences. A second run went even worse... Any feedback is appreciated.Comment
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Our run looked better, but not as good as I hoped for. Attached is a plot of the 2nd 260 bp read (the reverse read). (There should have been no complexity related problem with this library.)Comment
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Anyone know where this option is. I did a run the other day and I don't recollect a section on the software that allowed me to chose a matrix.Originally posted by behavin View PostComment
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The software upgrade to sequences 2x250 is now available.... the hardware to capture sequence from both sides of the flowcell i.e. double your total output, requires waiting on a list of MiSeq owners.Comment
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Ours was upgraded today. It even came with a thank you card!
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Yup. It's the little things that matter in life!Comment
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Ours was upgraded a few weeks ago, and I opened the upgrade box for a poke around before the FSE installed it... there was a sticker and a thank you card in the box, but it was never given to us *sniff sniff* :'-(Originally posted by james hadfield View PostLast edited by ScottC; 09-23-2012, 09:40 PM.Comment
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Hello everybody
Our Miseq will be updated next week, customer service said us that they don't make any Phix control run, only optic tests. Is there the same in your lab?Comment
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You may wish to invest in a phiX run. It can potentially save you time down the road.
Our upgraded MiSeq (which had passed optical tests), required a service call because a phiX run (done after the fact due to quality issues with samples) did not pass illumina quality standards.
Originally posted by jertlse View PostComment
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Ours didn't have a verification run (it was OK after the first run, too). They don't do it by default. If you're worried, then you can always ask Illumina for a sequencing kit to test the machine. Otherwise, if you do the recommended PhiX spike-in on your first run (if you don't do it routinely), then you can check the quality that way. I'm sure they will service the machine and replace the reagents if it's not up to scratch.Comment
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