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FelixKrueger / Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states
http://felixkrueger.github.io/Bismark/
GNU General Public License v3.0
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Expected unique alignment % #681

Closed gevro closed 2 days ago

gevro commented 2 days ago

Hi, What is the expected unique alignment %? For example, for NEB EM-seq libraries, I'm seeing only 60 - 75%, which seems low to me. This is with max insert size set to 1000.

FelixKrueger commented 2 days ago

This depends on several factors, naming just a few: the genome of interest and its repeat content, SE or PE, read length, contamination (adapter dimers, other organisms, out of control spike-ins, PhiX etc), and appropriate trimming. For human libraries with ~100bp reads PE I would probably expect around 80%, for mouse probably a little less

gevro commented 2 days ago

Thanks!