User: pierre.peterlongo

Reputation:
630
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Trusted
Location:
France
Website:
http://people.rennes.i...
Twitter:
pierre350d
Last seen:
5 days, 16 hours ago
Joined:
4 years, 9 months ago
Email:
p****************@inria.fr

about me

Posts by pierre.peterlongo

<prev • 91 results • page 1 of 10 • next >
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Answer: A: Calling SNPs with low coverage
... Hi there, Maybe it's a bit late, but I'd like to highlight the [discoSnp][1] approach which might answer this initial question. Without reference genome, discoSnp may predict SNPs and Indels from raw NGS reads. It does not depend on read alignment process and may find low covered variants. It rem ...
written 7 days ago by pierre.peterlongo630
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Answer: A: ID field of discosnp++
... Hi - If the VCF file was created with a reference genome, it may appear that some predicted variants are not mapped on the genome. If it was created without a reference genome, none of them are mapped. When a variant is not mapped to a reference genome, the chrom field indicates the id of the pre ...
written 20 days ago by pierre.peterlongo630
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Answer: A: GATB - create or manipulate data of Sequence
... Hi, From the GATB [documentation][1], you will find many [snipets][2] examples. You code could be #include Sequence str2seq(std::string str){ BankFasta dummyBank (str); BankFasta::Iterator it (dummyBank); for (it.first(); !it.isDone(); it.ne ...
written 28 days ago by pierre.peterlongo630
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Answer: A: Inserting k-mers into existing Graph with GATB
... 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 12 weeks ago by pierre.peterlongo630
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Comment: C: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
... 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 5 months ago by pierre.peterlongo630
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Answer: A: DiscoSNP++ 2.2.X VCF calls a A to an A SNP
... 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 5 months ago by pierre.peterlongo630
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Comment: C: DiscoSNP++ 2.2.X VCF calls a A to an A SNP
... Thanks for the input. We are currently working on this issue. We keep you in touch as soon as we have news. Pierre ...
written 5 months ago by pierre.peterlongo630
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Answer: A: DiscoSNP++ 2.2.X VCF calls a A to an A SNP
... 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 5 months ago by pierre.peterlongo630
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Comment: C: Problem with DiscoSNP KISSREADS module
... 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 17 months ago by pierre.peterlongo630
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Answer: A: Problem with DiscoSNP KISSREADS module
... 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 17 months ago by pierre.peterlongo630

Latest awards to pierre.peterlongo

Teacher 20 days ago, created an answer with at least 3 up-votes. For A: How to get the histogram of a graph
Scholar 28 days ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Popular Question 4 months ago, created a question with more than 1,000 views. For DiscoSnp becomes DiscoSnp++
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to get the histogram of a graph
Popular Question 15 months ago, created a question with more than 1,000 views. For DiscoSnp becomes DiscoSnp++
Scholar 17 months ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Scholar 2.0 years ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Scholar 2.0 years ago, created an answer that has been accepted. For A: discosnp contig extension on test dataset
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Inferring Novel Exons From Rna-Seq Data
Appreciated 2.1 years ago, created a post with more than 5 votes. For DiscoSnp++ 2.1.2 release: now genotypes and creates VCFs
Scholar 2.2 years ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Inferring Novel Exons From Rna-Seq Data
Supporter 2.2 years ago, voted at least 25 times.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For [no longer vacant] Postdoctoral Position (18 Months) - Inria Rennes - France
Popular Question 2.3 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 2.3 years ago, created a question with more than 1,000 views. For Postdoctoral Position (18 Months) - Inria Rennes - France
Scholar 2.3 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: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
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
Scholar 2.7 years ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Appreciated 2.7 years ago, created a post with more than 5 votes. For discoSnp - reference-free finding of isolated SNPs from non assembled reads
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: discosnp contig extension on test dataset
Appreciated 3.2 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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