User: pierre.peterlongo
pierre.peterlongo • 600
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Posts by pierre.peterlongo
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... Hi there,
This functionality is not realized and not adapted to the minia data structure, designed to the indexation of a fixed kmer set. ...
written 23 days ago by
pierre.peterlongo • 600
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... Hey,
Thanks for your suggestion. I may do the modification. However, I'm afraid that mapsembler would deserve a much deeper code update and review. Many users complain that compilation fails, depending on their OS and GCC version.
Anyone interested in the maintenance and update of the code is war ...
written 3 months ago by
pierre.peterlongo • 600
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... This issue was certainly due to a very rare case in which the two paths of a variant map the same locus but with very distinct alignment.
A fix is proposed in the commit from today: 4dda977dd7f357557e9b91b5fecae71e8606fab0
https://github.com/GATB/DiscoSnp/commit/4dda977dd7f357557e9b91b5fecae71e8606 ...
written 3 months ago by
pierre.peterlongo • 600
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... Thanks for the input.
We are currently working on this issue. We keep you in touch as soon as we have news.
Pierre ...
written 3 months ago by
pierre.peterlongo • 600
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... Hello all,
Sorry for this very late answer.
This is a strange unknown behaviour. Laeb, would you mind finding this variant in the ..._coherent.fa file (finding the variant id 410323) and showing this here so we could understand the issue?
Pierre ...
written 3 months ago by
pierre.peterlongo • 600
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... This is actually a solution.
The original call to discoSnp from Amel was not using correctly the argument for including read sets. This is why I developed here the way of using this argument. ...
written 15 months ago by
pierre.peterlongo • 600
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... Hi Amel, hi all,
Following an email discussion we found out that discoSnp was called using the following command:
`~/DiscoSnp/run_discoSnp++.sh -r filename1.fastq.gz filename2.fastq.gz -out output_SNP`
As expressed in the doc (*doc* directory) the read set(s) to use should be defined using a * ...
written 15 months ago by
pierre.peterlongo • 600
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Answer:
A: Problem compiling DiscoSNP
... Hi,
Sorry for the inconvenience. You don't need to be root to install discoSnp, the problem comes from something else. I never met the "Unmatch" problem.
Do you have cmake installed on the cluster?
What is your c++ compiler version?
Would you mind sending me exactly the commands you typed a ...
written 19 months ago by
pierre.peterlongo • 600
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Comment:
C: DiscoSnp becomes DiscoSnp++
... Hi Annick,
Thanks for your message and your patience :)
disco finds variants surrounded by at least k nucleotides left and right. By default, k=31 explaining why disco does not find results on your example.
Pierre
...
written 19 months ago by
pierre.peterlongo • 600
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Comment:
C: DiscoSnp++ Installation Problem
... Hi !
I'm discovering both your problem and its solution! Happy you fixed the issue, and sorry for this late reply :)
Pierre
...
written 20 months ago by
pierre.peterlongo • 600
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