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Old 08-20-2011, 04:58 AM   #1
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Location: CT, USA

Join Date: Jun 2011
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Default insert size question for sequencing

-I use 75X2 sequencing to get a good coverage.
-Meanwhile, I want a good coverage of different size: inset size from 40bp to 300bp.

My question is:
For the 75X2 sequencing, Can I sequence 40bp insert (40 bp DNA fragment within 2 ends' adapter sequencing)?

(I assume that for >75bp insert, sequencing should be no problem, and
I do not care that for 75x2 sequencing of 40bp, the sequencing read may contain adapter-sequence).

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Old 08-25-2011, 07:16 AM   #2
Location: Netherlands

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I think what is important here is the bridge amplification in the cluster formation.

I believe I heard/read somewhere that a total fragment length of 150 bp is the minimum for bridge formation (can anyone confirm this)? But with the Illumina adapters, I think your 40 bp insert will result in a total fragment size of about 150 bp (adapters are quite long), so I think that should not be a problem...
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Old 08-25-2011, 08:21 AM   #3
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Small inserts are not a problem, since adapter dimers are readily sequenced. I would recommend trimming the adapter sequences before starting any downstream analysis.

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