User: dlawre14

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dlawre1430
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United States
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2 years, 3 months ago
Joined:
3 years, 9 months ago
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d*******@slu.edu

Posts by dlawre14

<prev • 8 results • page 1 of 1 • next >
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Comment: C: More specifics on Jellyfish -C methodology.
... Ok so it's actually simple, they just count both and then group together the kmer and rc(kmer) and select lexicographically first as the "name" for that set. Thanks for all the help! ...
written 2.4 years ago by dlawre1430
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Comment: C: More specifics on Jellyfish -C methodology.
... Ok I think I understand most of this, but let me get a specific example, suppose we have `ATG` occurring `3` times and `CAT` occurring `2` times, what does this output as in jellyfish, is it `CAT> 5` or `ATG> 5` ...
written 2.4 years ago by dlawre1430
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More specifics on Jellyfish -C methodology.
... I know in Jellyfish `-C` stands for canonical kmers, however I'm a little iffy on how this is implemented. Does Jellyfish take into account whether the reads are paired-end or not? I'm working on my own kmer software to use internally and want the the results to be equivalent to what jellyfish would ...
kmer jellyfish written 2.4 years ago by dlawre1430 • updated 2.4 years ago by Rob3.4k
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Comment: C: Metagenome Read Simulators
... I hadn't thought of BBMap... I swear that thing does everything now. Thank you! ...
written 2.5 years ago by dlawre1430
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Metagenome Read Simulators
... I've been doing some research into simulators for simulating metagenomes and I cannot find a good consensus on what to use. The two big ones I've seen are MetaSim and BEAR. Does anyone have experience with these or others or have any advice for a good meta-genome simulator? ...
reads simulator metagenomics written 2.5 years ago by dlawre1430 • updated 2.5 years ago by genomax70k
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Comment: C: BLAST Score vs E-value in BioPython
... Ah thank you. I read the documentation and must have missed the hsp.expect choice for hsp records. Boy do I feel dumb. ...
written 3.8 years ago by dlawre1430
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Comment: C: BLAST Score vs E-value in BioPython
... I know from the blast side the difference between BLAST score and e-value, I was unclear on my call which value BioPython is calling hsps.score, is that equivalent to BLAST score? I am doing a machine learning project on protein function prediction and one of my methods is to align the subject again ...
written 3.8 years ago by dlawre1430
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BLAST Score vs E-value in BioPython
... When I use the following in BioPython     result.alignments[0].hsps[0].score What value is this? Is it the alignment score based on gap and mismatch penalties or the e-value? When using the above, is a larger number or a smaller number better? ...
biopython blast written 3.8 years ago by dlawre1430 • updated 3.8 years ago by Dan Gaston7.1k

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