User: DriesB

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DriesB10
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Leiden, The Netherlands
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Posts by DriesB

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Comment: C: Adapter trimming - Nextera XT dual indexes
... As I explain [below](https://www.biostars.org/p/195233/#399862), with artifact I mean adapter+ID+P5/P7. I think there's a risk that we're now repeating [the comment thread started by ATpoint](https://www.biostars.org/p/195233/#399844). ...
written 23 days ago by DriesB10
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Comment: C: Adapter trimming - Nextera XT dual indexes
... Okay, i was thinking of BBduk's [Usage Examples][1]; the first one uses `k=23` and `mink=11`. The adapter sequence above is too short to find adapters within the sequence, but what if the sequence is read further than the adapter, all the way into the index? Then `mink` is not useful either. ... Pe ...
written 24 days ago by DriesB10
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Comment: C: Adapter trimming - Nextera XT dual indexes
... Yes, Illumina supplies these adapter sequences, but how do you reconstruct the complete 'artifact' sequence from that? I've responded to ATpoint's comment about this ([below](https://www.biostars.org/p/195233/#399844)). I know that I'm not linking to the correct repository, but on SourceForge you c ...
written 24 days ago by DriesB10
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Comment: C: Adapter trimming - Nextera XT dual indexes
... Thank you for your comment! I may be indeed using the incorrect terminology here. With adapter, I meant the entire artifact, including index and p5/7. We're trimming away the entire artifact, right (although adapter already would suffice). Nextera's adapter sequence `CTGTCTCTTATACACATCT` ([source][ ...
written 24 days ago by DriesB10
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Comment: C: Adapter trimming - Nextera XT dual indexes
... I know that this question is old, but I wanted to include a more in-depth answer for future reference. ...
written 24 days ago by DriesB10
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Answer: A: Adapter trimming - Nextera XT dual indexes
... Removing adapters containing dual indexes is not trivial, as every adapter is specific for a sample. Illumina provides sequences for [adapter trimming][1] (thank you [candida.vaz][2]!), but for the example, Nextera XT, these are not very specific, as they are short. So I agree that BBMap's adapter ...
written 24 days ago by DriesB10
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Comment: C: What's more clear, loops or functions?
... Thank you for the explanation why functional programming is most often to be preferred over imperative programming! ...
written 9 months ago by DriesB10
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Comment: C: What's more clear, loops or functions?
... Yes, that's true! But readability still has highest priority for me. ...
written 12 months ago by DriesB10
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Forum: What's more clear, loops or functions?
... Hello all, I wanted to discuss a question with you that I've been asking myself during a project. In this project, I had to `read.table()` a great number of files from a large number of groups, which were provided to us by multiple research groups. As the data was provided in multiple formats tha ...
R forum coding style written 12 months ago by DriesB10 • updated 12 months ago by Istvan Albert ♦♦ 81k

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