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Old 07-12-2019, 01:56 PM   #6
SNPsaurus
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Location: Eugene, OR

Join Date: May 2013
Posts: 521
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Our local facility offers 2x300 v3 MiSeq runs with 25 million reads and a 2x150 v2 run with 15 million reads. If I didn't need the extra 10 million reads, I might be tempted to just do 2x150 and merge the two reads, and save 40% on the run costs. Did it look like you got a v3 or v2 run, based on the number of reads (or any other info)?

It sure sounds to me like they chose the wrong read length but maybe you can still use the data? I always find it is most important in these situations to figure out (with them) where the process went wrong to help in the future. Maybe they need to formalize how the runs are requested--if it is just an e-mail and some people say paired-end 300 bp (meaning total length of 300 bp) and others paired-end 300 bp (meaning 2 reads of 300 bp each) then they rely a key bit of info that is open to mis-interpretation.
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