User: pierre.peterlongo

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http://people.rennes.i...
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pierre350d
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about me

Posts by pierre.peterlongo

<prev • 103 results • page 1 of 11 • next >
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Answer: A: Using the ranking value to filter
... 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.peterlongo720
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Answer: A: artificial hybrid set for discoSNP
... 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.peterlongo720
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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.peterlongo720
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Answer: A: can discoSnp make the distinction between homeologous loci
... 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.peterlongo720
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Comment: C: DiscoSNP++: reducing missing data for heterozygous species
... 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.peterlongo720
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Answer: A: DiscoSNP++: reducing missing data for heterozygous species
... 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.peterlongo720
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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.peterlongo720
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Comment: C: discoSNP++ comparison of shared and unique variants between different samples wi
... 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.peterlongo720
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Comment: C: Understanding DiscoSNP++ output VCF file
... `./.` (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.peterlongo720
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Answer: A: Understanding DiscoSNP++ output VCF file
... 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.peterlongo720

Latest awards to pierre.peterlongo

Scholar 6 weeks ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Centurion 6 weeks ago, created 100 posts.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How to get the histogram of a graph
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to get the histogram of a graph
Scholar 5 months ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Popular Question 9 months ago, created a question with more than 1,000 views. For DiscoSnp becomes DiscoSnp++
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How to get the histogram of a graph
Popular Question 20 months ago, created a question with more than 1,000 views. For DiscoSnp becomes DiscoSnp++
Scholar 22 months ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Scholar 2.4 years ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Scholar 2.4 years ago, created an answer that has been accepted. For A: discosnp contig extension on test dataset
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Inferring Novel Exons From Rna-Seq Data
Appreciated 2.5 years ago, created a post with more than 5 votes. For DiscoSnp++ 2.1.2 release: now genotypes and creates VCFs
Scholar 2.6 years ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Inferring Novel Exons From Rna-Seq Data
Supporter 2.7 years ago, voted at least 25 times.
Popular Question 2.7 years ago, created a question with more than 1,000 views. For [no longer vacant] Postdoctoral Position (18 Months) - Inria Rennes - France
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Mapsembler2 targeted micro assembly and visualization of the local assembly graph
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Postdoctoral Position (18 Months) - Inria Rennes - France
Scholar 2.8 years ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Scholar 2.8 years ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Scholar 3.0 years ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Scholar 3.1 years ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Appreciated 3.1 years ago, created a post with more than 5 votes. For discoSnp - reference-free finding of isolated SNPs from non assembled reads
Scholar 3.2 years ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap

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