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Forum: Bioinformatics 07-07-2016, 03:00 PM
Replies: 11
Views: 2,353
Posted By Brian Bushnell
At the same time. When you tell BBDuk to do both...

At the same time. When you tell BBDuk to do both in one pass, it does quality-trimming after adapter-trimming, which is optimal. If you do quality-trimming first (with left-trim, as in qtrim=rl)...
Forum: Bioinformatics 07-07-2016, 02:19 PM
Replies: 11
Views: 2,353
Posted By Brian Bushnell
Oh, that's not good. You have a lot of adapter...

Oh, that's not good. You have a lot of adapter sequence, but unfortunately the read quality dropped to zero at the end and is generally terrible. That will make the data very hard to use for a...
Forum: Bioinformatics 07-07-2016, 10:45 AM
Replies: 11
Views: 2,353
Posted By Brian Bushnell
What kind of library/experiment is this? Also,...

What kind of library/experiment is this? Also, what does the quality profile look like? Posting the FastQC results would be helpful, for example. Running BBMerge for an insert size histogram could...
Forum: Bioinformatics 12-14-2015, 12:31 PM
Replies: 11
Views: 2,353
Posted By Brian Bushnell
Assuming you are doing left-trimming, then in the...

Assuming you are doing left-trimming, then in the above example, yes, those results are correct. You would get tg, ctg, and actg respectively.
Forum: Bioinformatics 12-14-2015, 10:22 AM
Replies: 11
Views: 2,353
Posted By Brian Bushnell
For Illumina reads, you don't need to worry about...

For Illumina reads, you don't need to worry about the edit distance, just hamming distance. BBDuk supports a variable hamming distance and variable kmer length, so the error rate would be the kmer...
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