Hi Brian,
I have started using BBDuk as it seemed more well documented and supported than alternatives, and alternatives did not function as I expected. Thanks for writing these tools.
Earlier in the thread you discuss kmer lengths:
I am wondering how I might use this in my context. I have methylation data that suffers from read-through into adapter. Basically the insert sizes are small due to fragmented nature of the DNA, so there is a lot of adapter contamination. I have tested a few values for kmer (15,20,25). Instead of this arbitrary choosing, could you give me an example of what 'error rates' I can use in my context? I have a downstream plot to essentially determine by eye if trimming of adapter is successful, but it would be nice to explain how we arrive at the kmer value which resolves our issue.
Thanks again for the tools,
Bruce.
I have started using BBDuk as it seemed more well documented and supported than alternatives, and alternatives did not function as I expected. Thanks for writing these tools.
Earlier in the thread you discuss kmer lengths:
Originally posted by Brian Bushnell
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Thanks again for the tools,
Bruce.
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