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Recent Activity
All posts created by susannepfeifer
| Link to this post | posted 08 Apr, 2020 22:10 | |
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Dear all, All three recommended software packages agree that our phage genome contains 4 tRNAs. The Bioinformatics Guide states that "the version of Aragorn that is within DNA Master does not call all the tRNAs, nor does it correctly trim the ends of the tRNAs that it does identify" and that "tRNAscan-SE is not as good as Aragorn at determining the correct ends of the tRNAs". Thus, am I correct in assuming that we should go ahead and change the tRNA coordinates in our final genome annotation to the Aragon v.1.2.38 calls? Thank you in advance for your help! Best, Susanne |
Posted in: tRNAs → tRNA start/stop coordinates
| Link to this post | posted 08 Apr, 2020 17:55 | |
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Dear all, As Newbler is deprecated, we assembled "our" phage genome in class using "minia" – a short-read assembler based on a de Bruijn graph. Our assembly looks similar to the one created using Newbler but is slightly shorter (141kb vs 151kb) - any idea why this might be the case? How can we find out what type of ends our genome has? Thank you in advance for your help! Best, Susanne |
Posted in: Newbler → Newbler vs minia