User: edrezen

gravatar for edrezen
edrezen670
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670
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France
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8 hours ago
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2 years, 10 months ago
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e******@irisa.fr

Posts by edrezen

<prev • 75 results • page 1 of 8 • next >
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Comment: C: Bug in JellyFish and DSK k-mer counting tool?
... DSK indeed will use a canonical form of the kmer that corresponds to the minimum value of the kmer and its reverse-complement. So in the example one should grep ACTTGCAGCCGCCACAATGGGTGTTATGTAA. ...
written 3 months ago by edrezen670
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Answer: A: Getting list of connected nodes to a node
... Hello, You could have a look [here][1], in particular the "successor" method of the Graph class. [1]: http://gatb-core.gforge.inria.fr/doc/api/snippets_graph.html#snippets_dbg_3 ...
written 5 months ago by edrezen670
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Comment: C: running SOAP using 32G RAM
... You can have a look [here][1] about Minia, in particular Table 2 to have an idea of memory usage of Minia. [1]: http://minia.genouest.org/ ...
written 6 months ago by edrezen670
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Comment: C: LoRDEC correction insufficient memory error
... The issue occurs during the kmer counting algorithm of the GATB library; I think this bug has been corrected in the latest version of the library 1.2.0. **However**, there are some API changes in the GATB library 1.2.0 so it is not usable as it with lordec. The best shot you have right now is to p ...
written 10 months ago by edrezen670
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Comment: C: Minia crashes during kmer counting
... You have a point here: for kmer size >= 128, the default algorithm of one part of the de Bruijn algorithm (cascading BLoom filters) can't work. In such a case, a specific option has to be used, ie. you should add **-debloom original** in your minia command line (the consequence is a bigger memo ...
written 10 months ago by edrezen670
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Comment: C: hash function for DNA sequences
... Take for instance the kmer K=GTCGAATC (size 8) If you take by convention A=0, C=1, G=2, T=3, you can encode K as a polynomial in base 4 like this: K = G.4^0 + T.4^1 + C.4^2 + G.4^3 + A.4^4 + A.4^5 + T.4^6 + C.4^7 K = 2*4^0 + 3*4^1 + 1*4^2 + 2*4^3 + 0*4^4 + 0*4^5 + 3*4^6 + 1*4^7 K = 28 ...
written 11 months ago by edrezen670
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Answer: A: problem compiling discoSnp++ make: *** No targets specified and no makefile fo
... Hello, DiscoSNP++ requires that the [cmake][1] tool is installed on your machine (see the trace "cmake: command not found") You have to install cmake first before building DiscoSNP++. [1]: https://cmake.org/ ...
written 12 months ago by edrezen670
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Comment: C: C++ tools are hard to install for biologist, why the community stick on it?
... I strongly agree with Rob's comment about the great control over memory coming with c++. Moreover, I am not sure at 100% that java takes advantage to use specific hardware features as SSE registers for instance (which allows to vectorize some algorithms with great speedups) Note that I am a great ...
written 12 months ago by edrezen670
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Comment: C: Internal memory allocator is full!
... Hello, I think you are using an old version of minia. You should have a try to the new one here (much faster with improved result quality); there are chances that you won't face the same memory issues with this new version. ...
written 13 months ago by edrezen670
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Comment: C: What tools you use or know for PacBio Long Read error correction?
... Just for information, the hyperlink for LoRDEC in your post (http://www.atgc-montpellier.fr/lordec/) does not seem to work (404 not found). ...
written 16 months ago by edrezen670

Latest awards to edrezen

Popular Question 10 months ago, created a question with more than 1,000 views. For KLAST, a Blast-like tool for fast sequence similarity searches: free academic version
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: hash function for DNA sequences
Scholar 20 months ago, created an answer that has been accepted. For A: k-mer tools - probability based models
Scholar 23 months ago, created an answer that has been accepted. For A: k-mer tools - probability based models
Scholar 23 months ago, created an answer that has been accepted. For A: k-mer tools - probability based models
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: k-mer tools - probability based models
Supporter 24 months ago, voted at least 25 times.
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: k-mer tools - probability based models
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: k-mer tools - probability based models
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: k-mer tools - probability based models
Scholar 2.6 years ago, created an answer that has been accepted. For A: k-mer tools - probability based models

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