User: Pierre
Pierre • 490
- Reputation:
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- Spain
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- 3 years, 8 months ago
- Joined:
- 9 years, 4 months ago
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Posts by Pierre
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... Glad that you dig the boosting.
About your question, I just tried it and could visualize all chromosomes. What problem do you face exactly? Is it with track visualization or tables?
Cheers
...
written 3.7 years ago by
Pierre • 490
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Answer:
A: Phased Data In Plink
... Thnaks,
we found a way in the meantime that may be useful:
you recode each diploid individual in 2 haploid ones
Ind1 Ind1 0 0 0 0 A T G C
Ind2 Ind2 0 0 0 0 G C A T
becomes
Ind1 Ind1_a 0 0 0 0 A A G G
Ind1 Ind1_b 0 0 0 0 T T C C
Ind2 Ind2_a 0 0 0 0 G G A A
Ind2 Ind2_b 0 0 0 0 C C T T
but yo ...
written 8.0 years ago by
Pierre • 490
• updated
6.3 years ago by
Giovanni M Dall'Olio ♦ 26k
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Comment:
C: Phased Data In Plink
... Thanks Stephanie. I could be an option BUT I think plink, in any case just mix up the phase. if you give the following simple command plink --file input --recode --out output (so nothing is done and there shouldn't be any differneces between input and output) the phases are lost anyway. So, ok there ...
written 8.2 years ago by
Pierre • 490
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8 follow
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... Hello everybody,
I wonder whether it exists an easy way to conserve haplotypes when proceeding some basic actions with plink. Is there any options? I couldn't find on my own.
The situation is as following: we have phased data. We use the .ped and .map format. We want to apply some filters (e.g kee ...
written 8.2 years ago by
Pierre • 490
• updated
8 months ago by
Shicheng Guo • 7.6k
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... no problem! It is just that I'm sure that is not a matter of software. ...
written 9.3 years ago by
Pierre • 490
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... But maybe both of you think that using the methods you speak about (haploview and HaploBlock) , I would not have to phase my genotypes at all levels and I can use the phased genotypes at the highest level (GLOBAL) to extract the phased genotypes at lower levels (for less snps and individuals). Maybe ...
written 9.3 years ago by
Pierre • 490
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... I'm not looking for a method for haplotype reconstruction... ...
written 9.3 years ago by
Pierre • 490
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... Oooops sorry I haven't been alerted that there was a comment to answer.
The inpout data is as following:
a genotypefile: for each individual 2 vector of A/T/G/C, one per chromosome
a (facultative) population file: where you precise the population code for each individual.
And that's it!
So I do not ...
written 9.3 years ago by
Pierre • 490
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... Here it is:
http://stephenslab.uchicago.edu/software.html
You have two quite similar software: PHASE and fastPHASE. The algorithm is a bit different in the second one which makes it faster although more approximative. ...
written 9.3 years ago by
Pierre • 490
Latest awards to Pierre
Appreciated
7.9 years ago,
created a post with more than 5 votes.
For A: Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Appreciated
7.9 years ago,
created a post with more than 5 votes.
For Reconstruction Of Haplotypes From The Genotypes On Snps
Good Question
7.9 years ago,
asked a question that was upvoted at least 5 times.
For Reconstruction Of Haplotypes From The Genotypes On Snps
Good Question
7.9 years ago,
asked a question that was upvoted at least 5 times.
For Compute Genetic Map
Good Answer
7.9 years ago,
created an answer that was upvoted at least 5 times.
For A: Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Popular Question
7.9 years ago,
created a question with more than 1,000 views.
For Reconstruction Of Haplotypes From The Genotypes On Snps
Popular Question
7.9 years ago,
created a question with more than 1,000 views.
For Compute Genetic Map
Popular Question
7.9 years ago,
created a question with more than 1,000 views.
For Phased Data In Plink
Teacher
7.9 years ago,
created an answer with at least 3 up-votes.
For A: Recommend Your Favorite Introductory "R In Bioinformatics" Books And Resources
Student
7.9 years ago,
asked a question with at least 3 up-votes.
For Reconstruction Of Haplotypes From The Genotypes On Snps
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