Minimal fragment size for GAIIx or HiSeq??

[Unununium]

Hi all,
is fragment size of 100 bp (before adapter ligation) to small to make "bridges" on the flow cell? Or is there any other issue why 100 bp should not be suitable?
Thanks!

[kmcarr]

A fragment size of 0 (zero) is sufficient for bridge amplification. I can attest to this having sequenced many primer-dimers. The only issue with a small insert is the limit on the number of cycles you can run without running into the downstream adapter. If your fragment size AVERAGE is 100bp then I would expect a significant fraction to be < 75bp. I probably wouldn't run longer than 55 cycles myself in this situation.

[cascoamarillo]

I hope is not! I've smaller fragment sizes

In general I was told that for PE Illumina recommend larger libraries for a variety of reasons, although the general range that people chose is somewhere between 250-600bp (no including the adapter sequences). But the ideal is to have a fragment size distribution as tight as possible (+/-25 bp) in order to achieve the highest level yield.
I think that for SR flowcell the optimun size could be smaller. But anyway, the bridge amplification will occur in the PE flowcell for this < 200 bp.

[cine]

will 100bp PE detect short transcripts e.g. &lt;100bp

Does this mean that short transcripts, say less than 100bp, will be detected using RNA-seq 100bp PE? But will this completely depends on the size range extracted from the gel and PCRed during sample prep?

Thanks