User: Pierre

gravatar for Pierre
Pierre490
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490
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Location:
Spain
Last seen:
3 years, 8 months ago
Joined:
9 years, 4 months ago
Email:
p***********@upf.edu

Posts by Pierre

<prev • 15 results • page 1 of 2 • next >
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Answer: A: A Database Of Signatures Of Selection In The 1000 Genomes Dataset
... 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 Pierre490
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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 Pierre490 • updated 6.3 years ago by Giovanni M Dall'Olio26k
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Comment: C: Phased Data In Plink
... I will check it out! ...
written 8.2 years ago by Pierre490
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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 Pierre490
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Phased Data In Plink
... 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 ...
plink genotyping written 8.2 years ago by Pierre490 • updated 8 months ago by Shicheng Guo7.6k
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Comment: C: Reconstruction Of Haplotypes From The Genotypes On Snps
... no problem! It is just that I'm sure that is not a matter of software. ...
written 9.3 years ago by Pierre490
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Answer: A: Reconstruction Of Haplotypes From The Genotypes On Snps
... 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 Pierre490
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Comment: C: Reconstruction Of Haplotypes From The Genotypes On Snps
... I'm not looking for a method for haplotype reconstruction... ...
written 9.3 years ago by Pierre490
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Comment: C: Reconstruction Of Haplotypes From The Genotypes On Snps
... 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 Pierre490
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Comment: C: Reconstruction Of Haplotypes From The Genotypes On Snps
... 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 Pierre490

Latest awards to Pierre

Appreciated 7.9 years ago, created a post with more than 5 votes. For Reconstruction Of Haplotypes From The Genotypes On Snps
Appreciated 7.9 years ago, created a post with more than 5 votes. For Compute Genetic Map
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
Student 7.9 years ago, asked a question with at least 3 up-votes. For Compute Genetic Map
Student 7.9 years ago, asked a question with at least 3 up-votes. For Phased Data In Plink

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