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Old 11-12-2014, 12:57 PM   #46
ysnapus
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Location: Mid-Atlantic

Join Date: Jun 2013
Posts: 22
Default bbduk2 and some clarifications

Thanks for bringing out a great tool. Noob here so please don't mind some questions, and I hope the answers will be of use to others as well.
  1. I noticed that there is a bbduk.sh and bbduk2.sh in the BBMap code I downloaded from Sourceforge. Is bbduk2 a replacement? Should we switch to using bbduk2.sh? Your example usage in this thread uses bbduk.sh.
  2. I have paired-end DNA Seq data, and I know there has been quite a lot of adapter readthrough since my read lengths are high and some inserts were small. Trimmomatic has the palindrome mode for adapter trimming in PE reads. Does bbduk do the palindromic alignment automatically or do we need to set tbo=t and tpe=t in command line parameters? If this is not what tbo is, what does tbo do?
  3. The usage help lists parameters like tbo=f, so to set it true you need tbo=t, but your example in a post lists it
    bbduk.sh ... tpe tbo.
    Is either usage correct?
  4. Am I correct in assuming that we just need to do ktrim=r, even for paired-end data, because of the opposite orientations of the paired reads?

Thank you.
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