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Old 10-12-2017, 07:28 AM   #52
Microalgues
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Location: Belgium

Join Date: Oct 2017
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Quote:
Originally Posted by GenoMax View Post
While Brian will have a more detailed insight it should be ok to use the unmasked genome with BBSplit. Any mapping issues you may have with short reads should be more or less same with genome or just CDS sequences.
Thanks GenoMax,

I see from other thread that masked genomes are used in order to prevent false positives when removing contamination.

At the same time in the thread you suggest simply use BBSplit, which should be enough.

Quote:
Originally Posted by GenoMax View Post
You can create them yourself using bbmask.sh. Not sure if you would need to if you are just looking to remove reads mapping to mito and chloroplast.

I assume you have seen BBsplit, which can be used for this purpose.
With thanks,
Xavier
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