Maximum fragment length

[Jenny Russ]

I plan to use Solexa in the near future. I want to sequence a full length cDNA library. I would like to know which fragment length can maximally be used with Solexa. Is it possible to work with cDNA with a length in the low kb area?

Jenny

[swbarnes2]

The limiting factor is generally thought to be the clustering process...If your fragments are large, they won't make nice looking, distinct clusters.

I think that some people have had luck with fragments in the low hundreds, up to high hundreds. I don't know how sucessful anyone has been with fragments larger than that.

[Chipper]

Why would you only like to sequence the ends of your cDNA?

[Jenny Russ]

I only want to sequence the end of the cDNAs because I do not need the whole sequence to identify them. I primarily want to quantify the cDNAs.
So it would be interesting for me to know up to which fragment length people successfully worked with Solexa.

Jenny

[ECO]

Sounds like you want to do SAGE.

[apfejes]

If it's not sage, maybe it's trying to be WTSS?

Admittedly, I work on the data processing side of things, so I may not understand what you're trying to do.... but why wouldn't you just sheer your fragments down even further, and then sequence that? I've seen successful runs with fragments of up to about 500bp, but have heard that fragments much larger than 600-700 bp tend to not work as well. (Second hand anecdotal information.)