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Old 07-01-2008, 01:36 PM   #1
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Location: CA

Join Date: Feb 2008
Posts: 4
Default Heavy read stacking on the solexa platform


Not sure if someone already brought this up here before, but has anyone looked into the heavy stacking problem that is evident on the Solexa (and SOLiD) platforms?

From the alignments, it is obvious that some regions have very deep coverage with reads starting and ending at the exact same position (This could be the same read replicated numerous times). This seems to be a library specific issue, and cannot all be accounted for by repeats. Some libraries are worse than others, and the situation is compounded most likely at the PCR step.

Has anyone worked on normalizing such reads? A simple collapsing to a consensus might result in loss of valid snp information. Besides one should be able to distinguish between valid coverage and stacking because of a bad library.

Any thoughts?

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