User: pierre.peterlongo

Reputation:
840
Status:
Trusted
Location:
France
Website:
http://people.rennes.i...
Twitter:
pierre350d
Last seen:
2 months, 2 weeks ago
Joined:
6 years, 7 months ago
Email:
p****************@inria.fr

about me

Posts by pierre.peterlongo

<prev • 109 results • page 1 of 11 • next >
1
vote
1
answer
331
views
1
answers
Answer: A: Haploid Genotypes in discoSNP++ VCFs
... Hi The genotyping is an option that can be switched off (`-n` option) when working on non diploid species. Computing the genotype on haploid species is meaningless. However, 0/1 results may warn you (depending on the effective coverage of each allele) as this may reflect the existence of approxim ...
written 12 months ago by pierre.peterlongo840
4
votes
1
answer
349
views
1
answers
Answer: A: DSK: readme and options
... Sebastien, You need to update your DSK version. [https://github.com/GATB/dsk/releases][1] [1]: https://github.com/GATB/dsk/releases ...
written 15 months ago by pierre.peterlongo840
1
vote
1
answer
349
views
1
answers
Comment: C: DSK: readme and options
... No its not a mistake Sebastien. Biostars is used as the canonical place to ask for questions regarding `GATB` tools. The developer team receives notifications for each new post that uses the `GATB` tag. You could have used the `dsk` tag though. ...
written 15 months ago by pierre.peterlongo840
0
votes
1
answer
440
views
1
answers
Answer: A: Perform of disco Snp with low coverage samples
... Hi Eric, You may try discoSnp, using all kmers (-c 1) but in this case, you not be able to make the difference between a real variant and a sequencing error in your data. You may also try to use kmers seen at least twice (-c 2). In this case you 'll miss all variants having coverage 1. The recall ...
written 15 months ago by pierre.peterlongo840
1
vote
1
answer
332
views
1
answers
Answer: A: Can DiscoSNP++ deal with hybrid input of both paired-end and single-end reads?
... Hi Emeline, The answer depends on what you want to use for calling variants and what you want to use for allele frequency computation. If you want to considere all your reads as a single set (no differentiation at all): * fof_root.txt: * fof.txt * fof.txt: * collapsed.fq.gz * pair1.truncate ...
written 15 months ago by pierre.peterlongo840
4
votes
2
answers
310
views
2
answers
Answer: A: Mapping variants to a reference genome discosnprad
... Hi there, Thanks for your question et remarks. **About the -G flag.** Indeed, we removed the variant mapping of ref process in the discoRad tool. This is a matter of time before we propose this back in discoRad. By the way, you may still use the `run_VCF_creator.sh` script on your .fa file gener ...
written 15 months ago by pierre.peterlongo840
1
vote
1
answer
293
views
1
answers
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 17 months ago by pierre.peterlongo840
0
votes
1
answer
342
views
1
answers
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 17 months ago by pierre.peterlongo840
2
votes
2
answers
471
views
2
answers
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 18 months ago by pierre.peterlongo840
1
vote
1
answer
481
views
1
answers
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 18 months ago by pierre.peterlongo840

Latest awards to pierre.peterlongo

Popular Question 9 months ago, created a question with more than 1,000 views. For DiscoSnp++ 2.2.0 release
Scholar 12 months ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Scholar 15 months ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to get the histogram of a graph
Scholar 15 months ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: How to get the histogram of a graph
Scholar 18 months ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Centurion 18 months ago, created 100 posts.
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: How to get the histogram of a graph
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: How to get the histogram of a graph
Scholar 23 months ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Popular Question 2.2 years ago, created a question with more than 1,000 views. For DiscoSnp becomes DiscoSnp++
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: How to get the histogram of a graph
Popular Question 3.1 years ago, created a question with more than 1,000 views. For DiscoSnp becomes DiscoSnp++
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
Scholar 3.8 years ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Scholar 3.8 years ago, created an answer that has been accepted. For A: discosnp contig extension on test dataset
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Inferring Novel Exons From Rna-Seq Data
Appreciated 4.0 years ago, created a post with more than 5 votes. For DiscoSnp++ 2.1.2 release: now genotypes and creates VCFs
Scholar 4.0 years ago, created an answer that has been accepted. For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Inferring Novel Exons From Rna-Seq Data
Supporter 4.1 years ago, voted at least 25 times.
Popular Question 4.1 years ago, created a question with more than 1,000 views. For [no longer vacant] Postdoctoral Position (18 Months) - Inria Rennes - France
Popular Question 4.2 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 4.2 years ago, created a question with more than 1,000 views. For Postdoctoral Position (18 Months) - Inria Rennes - France

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1781 users visited in the last hour