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Forum: Bioinformatics 07-30-2015, 10:05 AM
Replies: 347
Views: 185,344
Posted By bruce01
Hi Brian, to clarify, I did have mink=5 for...

Hi Brian,

to clarify, I did have mink=5 for the rest of the runs based on my previous assertion that SNP, methylation would not be called in the first/final 5bp of a read, so the 'mm' would have...
Forum: Bioinformatics 07-30-2015, 07:56 AM
Replies: 347
Views: 185,344
Posted By bruce01
Hi Brian, thanks for the reply. I have gone...

Hi Brian,

thanks for the reply. I have gone about testing different kmer to see what they result in in terms of retained bases. My thinking was that lower kmer should result in retaining less...
Forum: Bioinformatics 07-29-2015, 04:33 AM
Replies: 347
Views: 185,344
Posted By bruce01
Hi Brian, I have started using BBDuk as it...

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.

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