User: Maxime Lamontagne

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http://www.criucpq.ula...
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Posts by Maxime Lamontagne

<prev • 136 results • page 1 of 14 • next >
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Answer: A: Merge ped files in PLINK
... Try the merge option : https://www.cog-genomics.org/plink2/data#merge ...
written 9 weeks ago by Maxime Lamontagne1.8k
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Comment: C: Sorted hetamap using R
... I think you need to order the data yourself before making the heatmap. Also, sorted based on expression is unclear. ...
written 10 weeks ago by Maxime Lamontagne1.8k
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Answer: A: Mirror Manhattan Plot
... Did you try to invert the ylim option. Intead of c(0,10) for example, try c(10,0). ...
written 12 weeks ago by Maxime Lamontagne1.8k
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Comment: C: Calculate pairwise LD for two given genomic loci (not rsIDs)?
... **1- Input file** : If you have your own data (which you should always specify when you ask a question), replace "ALL.chr5.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" with your vcf file. **2- LD** : Yes, vcftools will calculate the LD for all coordinate pairs in the region. If ...
written 12 weeks ago by Maxime Lamontagne1.8k
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Comment: C: Calculate pairwise LD for two given genomic loci (not rsIDs)?
... **Example** vcftools --gzvcf ALL.chr5.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --chr 5 --from-bp 1000000 --to-bp 1100000 --out chr5_analysis --keep Samples.txt --hap-r2 **input_data.vcf** You can use vcf files from 1000 Genomes Project (ftp://ftp.1000genomes.ebi.ac.uk/vol ...
written 12 weeks ago by Maxime Lamontagne1.8k
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Answer: A: Calculate pairwise LD for two given genomic loci (not rsIDs)?
... If you don't have any data, you could download genotypes from the 1000 Genomes Project with tabix (http://www.internationalgenome.org/category/tabix/) and then use Haploview to calculate the LD. ...
written 12 weeks ago by Maxime Lamontagne1.8k
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Answer: A: How do you annotate microarray probes?
... On the GPL6246 platform page on GEO (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6246 ), at the bottom, press "Download full table". ...
written 8 months ago by Maxime Lamontagne1.8k • updated 8 months ago by genomax226k
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Comment: C: PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
... Try with the "--missing-genotype -9" option. ...
written 9 months ago by Maxime Lamontagne1.8k
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Answer: A: Plink --freq case-control output format
... [https://www.cog-genomics.org/plink2/formats#frq_cc][1] CHR Chromosome code SNP Variant identifier A1 Allele 1 (usually minor) A2 Allele 2 (usually major) MAF_A Allele 1 frequency in cases (Affected) MAF_U Allele 1 frequency in controls (Unaffected) NCHROBS_A Number of case allele observation ...
written 11 months ago by Maxime Lamontagne1.8k
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Comment: C: Converting SNP from chr:pos to rs number using PLINK?
... You have two possible solution. 1) Do not update any SNP with two or more possible rs. It's not perfect, but it's a good temporary solution. 2) Find the good rs by comparing alleles. On UCSC, you can download alleles for each snp. Then choose the right rs. ...
written 13 months ago by Maxime Lamontagne1.8k

Latest awards to Maxime Lamontagne

Commentator 7 days ago, created a comment with at least 3 up-votes. For C: Plink: Quick Way To Combine Two Datasets Using Only Common Markers
Good Answer 24 days ago, created an answer that was upvoted at least 5 times. For A: Minor allele frequency calculation
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Appreciated 7 months ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Popular Question 7 months ago, created a question with more than 1,000 views. For How To Get Articles For A Snps List?
Popular Question 8 months ago, created a question with more than 1,000 views. For How To Get Articles For A Snps List?
Popular Question 10 months ago, created a question with more than 1,000 views. For Plotting Human Karyotype - Software
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Appreciated 14 months ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Minor allele frequency calculation
Epic Question 18 months ago, created a question with more than 10,000 views. For Bioinformatic Cartoon
Popular Question 19 months ago, created a question with more than 1,000 views. For Post-Doctoral - Genomic Research Program On Cardio-Respiratory Diseases - Quebec City
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Popular Question 20 months ago, created a question with more than 1,000 views. For Plotting Human Karyotype - Software
Scholar 21 months ago, created an answer that has been accepted. For A: Plink MAF Calculation
Appreciated 24 months ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Plotting Human Karyotype - Software
Centurion 2.1 years ago, created 100 posts.
Scholar 2.1 years ago, created an answer that has been accepted. For A: Minor allele frequency calculation
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Plotting Human Karyotype - Software
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Scholar 2.4 years ago, created an answer that has been accepted. For A: Minor allele frequency calculation

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