User: Rayan Chikhi
Rayan Chikhi • 1.4k
- Reputation:
- 1,450
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- Location:
- France, Lille, CNRS
- Website:
- http://twitter.com/Ray...
- Last seen:
- 7 months, 2 weeks ago
- Joined:
- 7 years, 5 months ago
- Email:
- r******@gmail.com
Posts by Rayan Chikhi
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0
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answer
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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 months ago by
Rayan Chikhi • 1.4k
3
votes
1
answer
214
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1
answers
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 months ago by
Rayan Chikhi • 1.4k
0
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4
answers
7.0k
views
4
answers
... 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 12 months ago by
Rayan Chikhi • 1.4k
• updated
8 months ago by
RamRS ♦ 25k
0
votes
1
answer
524
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1
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... 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 18 months ago by
Rayan Chikhi • 1.4k
1
vote
1
answer
419
views
1
answers
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 18 months ago by
Rayan Chikhi • 1.4k
2
votes
1
answer
419
views
1
answers
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 20 months ago by
Rayan Chikhi • 1.4k
1
vote
1
answer
2.0k
views
1
answers
... 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 21 months ago by
Rayan Chikhi • 1.4k
2
votes
2
answers
1.9k
views
2
answers
... Have a look at https://github.com/rrwick/Unicycler ...
written 22 months ago by
Rayan Chikhi • 1.4k
5
votes
1
answer
2.0k
views
1
answers
... "You won't believe what happened to this PhD student after he ran fastq-dump" ...
written 22 months ago by
Rayan Chikhi • 1.4k
0
votes
1
answer
613
views
1
answers
... Good to know the assembly completed with the latest version. Did you compare contigs between those two runs, or scaffolds? ...
written 24 months ago by
Rayan Chikhi • 1.4k
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7 months ago,
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For A: Choosing K-mer size in Kmergenie for denovo assembly
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Choosing K-mer size in Kmergenie for denovo assembly
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For Fast kmer reverse complement code using bit tricks
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18 months ago,
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For A: Choosing K-mer size in Kmergenie for denovo assembly
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22 months ago,
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For C: confusion in the DeBruijn Graph
Teacher
2.0 years ago,
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For A: How to determine appropriate value for abundance parameter?
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For A: Choosing K-mer size in Kmergenie for denovo assembly
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2.3 years ago,
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For A: Choosing K-mer size in Kmergenie for denovo assembly
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2.7 years ago,
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For Fast kmer reverse complement code using bit tricks
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For C: Kmergenie histogram file
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For Fast kmer reverse complement code using bit tricks
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For A: How to determine appropriate value for abundance parameter?
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For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
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3.8 years ago,
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For Larger-Than-Expected Total Scaffolds Size Using Nextera Mate Pairs
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For A: How to determine appropriate value for abundance parameter?
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For A: Choosing K-mer size in Kmergenie for denovo assembly
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4.9 years ago,
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For A: Illumina Assembly Gap Closure
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For C: Kmergenie histogram file
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