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Old 04-27-2009, 12:54 PM   #6
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
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Originally Posted by lh3 View Post
For short reads, proper pairing increases the coverage of the genome and substantially reduce false alignments.
The above is exactly right, although it may depend on the exact experiment. For example cancer sequencing we expect many translocations, or large-scale rearrangements, and preferring "paired reads" may reduce our power.

In general, if an aligner produces all hits for each end, any post-alignment filtering is possible (all the above classes). Of course some limit must be placed on the number of hits returned (thousands is overkill), since my 4 petabyte array of solid state hard drives has yet to arrive in the mail.
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