Removal of large fragments?

[seqAll]

Is it necessary to remove large fragments from the library?

The amplification, emPCR or bridge PCR, is able to generate amplicons longer than 1kb. During sequencing, would these long amplicons interfere with neighbouring wells or clusters?

Or is it because the shearing step make ALMOST all fragments short? Could a small portion of long fragments make substantial trouble in sequencing?

Anyone has done addtional step to remove the long ones?

[xenia.zhang]

i believe those large fragments are removed from size selection step when you cut bands of small size from gel, right?

[seqAll]

Sorry, I was not clear.

We normally do AMpure beads selection for small size frags. We used gel cut only once in the very beginning, and never do that again.