User: Rayan Chikhi

gravatar for Rayan Chikhi
Rayan Chikhi1.4k
Reputation:
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Location:
France, Lille, CNRS
Website:
http://twitter.com/Ray...
Last seen:
1 month, 2 weeks ago
Joined:
6 years, 11 months ago
Email:
r******@gmail.com

Posts by Rayan Chikhi

<prev • 222 results • page 1 of 23 • next >
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Comment: C: GATB-core kmer couting
... If you can tolerate that some of the answers for query k-mers will be wrong: then you can use GATB as-is and it will often return the right answer, but with a small probability (can be tuned to be arbitrarily very small) GATB will return that a k-mer is present in the graph when in fact it is not. ...
written 7 weeks ago by Rayan Chikhi1.4k
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Answer: A: GATB-core kmer couting
... Hi, Yes it's possible in GATB but you'd need to build a de Bruijn graph first. See this example: https://github.com/GATB/gatb-core/blob/master/gatb-core/examples/debruijn/debruijn26.cpp Note that this mechanism doesn't allow to determine if a k-mer is truly in the graph or not. GATB will return th ...
written 7 weeks ago by Rayan Chikhi1.4k
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Comment: C: Back Translating Protein Sequence Without Ambiguities...
... great code! Just a small bug that affects the behavior of `ambiguous_bases_reversed` (when a `T` is given to that dict), to fix it, delete the following line: frozenset(['U']): 'T', ...
written 6 months ago by Rayan Chikhi1.4k • updated 9 weeks ago by RamRS23k
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Answer: A: Segmentation fault when running Minia v3 with some kmer values
... Hi, Segfault is unlikely a memory error but rather a bug in the program or something else. Do you have enough disk space? Would it be possible to share the input data? Best, Rayan ...
written 12 months ago by Rayan Chikhi1.4k
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Comment: C: GATB buildNode giving errors
... Hi, sorry I didn't get notified by the responses in this thread. In the future, please reach me at rayan.chikhi@univ-lille.fr if this happens! 1) Are you using the Graph or GraphUnitigs class? (seems that it is GraphUnitigs) 2) If you're using GraphUnitigs, the function you're looking for is debug ...
written 12 months ago by Rayan Chikhi1.4k
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Answer: A: GATB buildNode giving errors
... Hi, could you try changing "Node left" to "auto left" to see if it gets rid of the error? Best, Rayan ...
written 14 months ago by Rayan Chikhi1.4k
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Comment: C: Want to use fastq-dump to download pacbio data? Read this before
... I think Bastien wants to know why we think the output of fastq-dump is "wrong". I recall it has to do with how the raw .bax.h5 PacBio files get converted to FASTQ. There seems to be additional step(s) needed in order to split raw reads and avoid chimeric reads. `dextractor` does them, but `fastq-dum ...
written 15 months ago by Rayan Chikhi1.4k
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Answer: A: Hybrid assembly using MinION data + correction with Illumina. Which strategy to
... Have a look at https://github.com/rrwick/Unicycler ...
written 16 months ago by Rayan Chikhi1.4k
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Comment: C: Want to use fastq-dump to download pacbio data? Read this before
... "You won't believe what happened to this PhD student after he ran fastq-dump" ...
written 16 months ago by Rayan Chikhi1.4k
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Comment: C: Minia assembler restart after error?
... Good to know the assembly completed with the latest version. Did you compare contigs between those two runs, or scaffolds? ...
written 18 months ago by Rayan Chikhi1.4k

Latest awards to Rayan Chikhi

Scholar 7 weeks ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Choosing K-mer size in Kmergenie for denovo assembly
Appreciated 7 months ago, created a post with more than 5 votes. For Fast kmer reverse complement code using bit tricks
Scholar 12 months ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: confusion in the DeBruijn Graph
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Scholar 18 months ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Scholar 21 months ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Fast kmer reverse complement code using bit tricks
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Kmergenie histogram file
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Fast kmer reverse complement code using bit tricks
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Good Answer 3.2 years ago, created an answer that was upvoted at least 5 times. For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
Scholar 3.3 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Guru 3.5 years ago, received more than 100 upvotes.
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
Appreciated 4.2 years ago, created a post with more than 5 votes. For GATB will provide developer support via Biostar
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: How to determine appropriate value for abundance parameter?
Scholar 4.4 years ago, created an answer that has been accepted. For A: Choosing K-mer size in Kmergenie for denovo assembly
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Illumina Assembly Gap Closure
Commentator 4.4 years ago, created a comment with at least 3 up-votes. For C: Kmergenie histogram file
Appreciated 4.5 years ago, created a post with more than 5 votes. For Fast kmer reverse complement code using bit tricks
Centurion 4.5 years ago, created 100 posts.
Appreciated 4.9 years ago, created a post with more than 5 votes. For GATB will provide user support via Biostar

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