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Forum: Illumina/Solexa 09-09-2016, 08:07 AM
Replies: 8
Views: 3,588
Posted By fanli
Sorry, yes. 211 bases in the middle - math is...

Sorry, yes. 211 bases in the middle - math is hard :/
Forum: Illumina/Solexa 09-09-2016, 08:01 AM
Replies: 8
Views: 3,588
Posted By fanli
They are merged as well - the full 291bp sequence...

They are merged as well - the full 291bp sequence from your original post is what you get. Another way to think about this is that you are sequencing a 251bp amplicon with 20 bases on each end unique...
Forum: Illumina/Solexa 09-09-2016, 07:54 AM
Replies: 8
Views: 3,588
Posted By fanli
I think we're in agreement - does the attached...

I think we're in agreement - does the attached diagram help?
Forum: Illumina/Solexa 09-09-2016, 07:29 AM
Replies: 8
Views: 3,588
Posted By fanli
What are your primer sequences? Are they on each...

What are your primer sequences? Are they on each end of the merged 291bp contig? From what you're saying, it sounds to me like 291 - 20 - 20 = 251...

Relatedly, you really should only have 2x250,...
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