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Old 02-07-2017, 01:39 PM   #420
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Originally Posted by Brian Bushnell View Post
How are the ORFs indicated? Do you have them in a separate file (gff/gtf/bed)? BBMap doesn't use any of those, though you could probably use a different tool to mask the reference with them. Generally, I don't recommend constraining alignment to a specific subset of the genome, which incurs confirmation bias.
I tried to simply use the multi-fasta format with the hope that the sequences would be seen as seperate and not connected:

But after randomising the order withing the ref file the coverage changed.
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