User: pierre.peterlongo
pierre.peterlongo • 830
- Reputation:
- 830
- Status:
- Trusted
- Location:
- France
- Website:
- http://people.rennes.i...
- Twitter:
- pierre350d
- Last seen:
- 2 months, 2 weeks ago
- Joined:
- 6 years ago
- Email:
- p****************@inria.fr
about me
Posts by pierre.peterlongo
<prev
• 109 results •
page 1 of 11 •
next >
1
vote
1
answer
178
views
1
answers
... 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 5 months ago by
pierre.peterlongo • 830
4
votes
1
answer
251
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 8 months ago by
pierre.peterlongo • 830
1
vote
1
answer
251
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 8 months ago by
pierre.peterlongo • 830
0
votes
1
answer
253
views
1
answers
... 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 8 months ago by
pierre.peterlongo • 830
1
vote
1
answer
204
views
1
answers
... 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 8 months ago by
pierre.peterlongo • 830
4
votes
2
answers
206
views
2
answers
... 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 8 months ago by
pierre.peterlongo • 830
1
vote
1
answer
204
views
1
answers
... 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 10 months ago by
pierre.peterlongo • 830
0
votes
1
answer
225
views
1
answers
... 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 10 months ago by
pierre.peterlongo • 830
2
votes
2
answers
368
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 11 months ago by
pierre.peterlongo • 830
1
vote
1
answer
363
views
1
answers
... 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 11 months ago by
pierre.peterlongo • 830
Latest awards to pierre.peterlongo
Scholar
5 months ago,
created an answer that has been accepted.
For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Scholar
8 months ago,
created an answer that has been accepted.
For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: How to get the histogram of a graph
Scholar
8 months ago,
created an answer that has been accepted.
For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: How to get the histogram of a graph
Scholar
11 months ago,
created an answer that has been accepted.
For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Centurion
11 months ago,
created 100 posts.
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: How to get the histogram of a graph
Teacher
15 months ago,
created an answer with at least 3 up-votes.
For A: How to get the histogram of a graph
Scholar
16 months ago,
created an answer that has been accepted.
For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Popular Question
19 months ago,
created a question with more than 1,000 views.
For DiscoSnp becomes DiscoSnp++
Teacher
2.3 years ago,
created an answer with at least 3 up-votes.
For A: How to get the histogram of a graph
Popular Question
2.5 years ago,
created a question with more than 1,000 views.
For DiscoSnp becomes DiscoSnp++
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
3.3 years ago,
created an answer that has been accepted.
For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Scholar
3.3 years ago,
created an answer that has been accepted.
For A: discosnp contig extension on test dataset
Teacher
3.3 years ago,
created an answer with at least 3 up-votes.
For A: Inferring Novel Exons From Rna-Seq Data
Appreciated
3.4 years ago,
created a post with more than 5 votes.
For DiscoSnp++ 2.1.2 release: now genotypes and creates VCFs
Scholar
3.5 years ago,
created an answer that has been accepted.
For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Teacher
3.5 years ago,
created an answer with at least 3 up-votes.
For A: Inferring Novel Exons From Rna-Seq Data
Supporter
3.5 years ago,
voted at least 25 times.
Popular Question
3.5 years ago,
created a question with more than 1,000 views.
For [no longer vacant] Postdoctoral Position (18 Months) - Inria Rennes - France
Popular Question
3.6 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
3.6 years ago,
created a question with more than 1,000 views.
For Postdoctoral Position (18 Months) - Inria Rennes - France
Scholar
3.6 years ago,
created an answer that has been accepted.
For A: Mapsembler2 targeted micro assembly and visualization of the local assembly grap
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1836 users visited in the last hour