User: pierre.peterlongo
pierre.peterlongo • 720
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Posts by pierre.peterlongo
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1
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... Hello Vanessa,
The rank value applies only "*when two or more read sets are used*". If you want to use the rank for filtering results, you may, indeed work with all your individuals together.
Best, Pierre ...
written 12 days ago by
pierre.peterlongo • 720
0
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70
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... Hi (again) andré,
Thanks for your question.
There was a bug in the script run_VCF_creator.sh (which was searching for the pattern "sam" in the .fa file nam).
This is now fixed and pushed in commit [012586e8411743e740887a5af53d7a9309b11e9a][1]
Sorry about the inconvenience.
[1]: https://gith ...
written 23 days ago by
pierre.peterlongo • 720
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Answer:
A: New To DiscoSnp-RAD
... Hi all,
This code comes from the supp mat of the original paper where we explained how experiments were conducted.
discoSnp (discoSnpRad or discoSnp++) takes as input read files organized in *file of files*. The idea (described in the documentation) is that a fof contains a list of read files.
...
written 6 weeks ago by
pierre.peterlongo • 720
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... Hello Yahan,
Thanks for your question here.
Generally speaking, discoSnp confuses true variants with inter-repetition or inter-genome variations.
There are then several ways of sorting out the true and false positives calls.
- One expects that true variants discriminate individuals and thus ...
written 6 weeks ago by
pierre.peterlongo • 720
0
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1
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174
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... Hi, sorry for the delay,
On regions with high variant density, discoSnp results depend on the 'b' option. With b 0 no variant is detected, with b 1 some of them are detected, and with b 2 almost all of them are detected (but with a high false positive rate on complex data).
Once detected, we can ...
written 10 weeks ago by
pierre.peterlongo • 720
0
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1
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... Hi Yann,
I do not understand why this is an issue. Are you expecting those variants to be covered?
The advice I can give you is to have a look to coverages themselves instead of genotype only. The threshold used to determine whether a variant is missing ./. or not depends on the *solidity thresh ...
written 10 weeks ago by
pierre.peterlongo • 720
0
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1
answer
161
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1
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Answer:
A: rank = 0 in DiscoSNP
... Hello,
The rank value reflects how discriminant a variant is among a set of individuals (read sets).
- If you've a unique read set, all rank value will be equal to zero, and this value is not informative
- else, variants whose rank is equal to zero are variants that do not discriminate read set ...
written 11 weeks ago by
pierre.peterlongo • 720
0
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1
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302
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... Hi André,
Your question is not clear to me, but I'm trying to answer it there:
There is a threshold applied on kmers abundance (kmer seen less than T times are not considered in the graph) and there is a threshold for read coherency (once reads are mapped back on alleles, we verify that each all ...
written 3 months ago by
pierre.peterlongo • 720
0
votes
2
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277
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... `./.` (for read set `i`): the variant whose id is *SNP_higher_path_9480770* has not enough corresponding reads in the read set `i`.
*not enough* means that both alleles are not read coherent (cf *read coherent* definition in the publication)
Pierre ...
written 4 months ago by
pierre.peterlongo • 720
3
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277
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... Hi Achal, thanks for your question.
Here is an explanation (non limited to discoSnp, and adapted to diploid species).
A genotype provides a way to know for each variant if it exists in the reference allele and/or in the alternative allele.
- with a `/` :
- with a reference genome: the first ...
written 4 months ago by
pierre.peterlongo • 720
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