User: pierre.peterlongo
pierre.peterlongo • 860
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Posts by pierre.peterlongo
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... 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 17 months ago by
pierre.peterlongo • 860
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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 20 months ago by
pierre.peterlongo • 860
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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 20 months ago by
pierre.peterlongo • 860
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... 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 20 months ago by
pierre.peterlongo • 860
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... 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 20 months ago by
pierre.peterlongo • 860
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... 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 20 months ago by
pierre.peterlongo • 860
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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 22 months ago by
pierre.peterlongo • 860
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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 months ago by
pierre.peterlongo • 860
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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 23 months ago by
pierre.peterlongo • 860
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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 23 months ago by
pierre.peterlongo • 860
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