insert size question for sequencing

[xp8]

-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).

Thanks
Victor

[hbn]

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...

[HESmith]

Small inserts are not a problem, since adapter dimers are readily sequenced. I would recommend trimming the adapter sequences before starting any downstream analysis.

-Harold