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Old 05-08-2017, 04:05 PM   #15
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Join Date: Apr 2017
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Originally Posted by Brian Bushnell View Post
If you plan to normalize the reads after mapping but before assembly anyway, then yes, it's logical to just map with the normalized reads... but only if the reads were normalized together (which they probably weren't). If they were normalized independently, you need to either combine them all, then normalize, then map, or map, then combine them all, then normalize. Normalizing independently will lose the low-coverage part of each library (depending on your settings) that could still be assembled once the libraries are combined.
Thanks for the reply. The reads were indeed normalized together after following your suggestion. Took about 5 days to go through 7 TB of data which is faster than i expected. I still want to approximate "co-assemble" strategy as best as I can even if I can't assemble the normalized reads directly.
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