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Old 07-23-2013, 07:44 AM   #2
JamieHeather
@jamimmunology
 
Location: London

Join Date: Nov 2012
Posts: 96
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I recently had my first play with combining overlapping reads (as detailed in this thread).

I was trying to overlap amplicons of one of two lengths, sequenced on a MiSeq v2 2x251 kit. Bottom line, the 420bp fragments overlapped great, the 320bp fragments wouldn't combine at all (unless I trimmed the reads down a bit so that one read wasn't extending past the start point of the other).

So at the very least, an overlap ~70bp is plenty to get > 90 % of reads overlapping (note that the mean quality at the end of my reads is still > Q20, just).
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