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Old 07-12-2019, 03:49 PM   #7
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Location: US

Join Date: Apr 2013
Posts: 222

Originally Posted by SNPsaurus View Post
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.
Hmm, interesting. I didn't realize MiSeq has 2X150bp runs choice. Again, this is new sequencing center. My previous center for Amplicon sequencing only has 2X300bp or default is this settings. I am not sure if I could use this data.

As you know my amplicon is about 290 bp. If I use 300bpX2, it perfectly covers the whole amplicon twice (F and R). However, if it is 150bp X 2, even if I could join F and R reads together, it only has <50bp overlapped fragment, it won't join very well. If I don't join this, I only have 150 bp information and I lost half of them. Why would I originally brother to choose 290 size amplicons.

As you know, it is not Shortgun genomics, which shorter reads or longer reads may have different advantage in assembly etc.
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