User: Maxime Lamontagne

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Posts by Maxime Lamontagne

<prev • 151 results • page 1 of 16 • next >
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Comment: C: PLINK .bim file shows chromosome 0 on Affymetrix chip
... Did you try the --exclude option in PLINK? ...
written 18 days ago by Maxime Lamontagne1.9k
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Comment: C: What people do with the probes that doesn't have any GENE SYMBOL in annotation d
... I think this paper is doing exactly what you want. > Framework for reanalysis of publicly available Affymetrix® GeneChip® > data sets based on functional regions of interest https://www.biorxiv.org/content/biorxiv/early/2017/04/11/126573.full.pdf ...
written 26 days ago by Maxime Lamontagne1.9k
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Answer: A: What does people do with the probes that doesn't have any GENE SYMBOL in annotat
... It’s not unusual in older array. Due to changes in gene annotation and reference sequence, some probe set may be outdated (probes not mapping to any gene in the new build). To find a gene for your probe set, you need to blat all the probes of the probe set and look where they are mapping. ​ ...
written 27 days ago by Maxime Lamontagne1.9k
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Answer: A: literature review by a web server
... [IBioGuide][1] could hep you. [1]: https://www.advaitabio.com/ibioguide.html ...
written 8 weeks ago by Maxime Lamontagne1.9k
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Answer: A: logistic regression with PLINK
... Maybe the "--freq" command will give you this info. ...
written 9 weeks ago by Maxime Lamontagne1.9k
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Comment: C: Using Plink, get allele frequencies for a subset of individuals
... I gues one of your file is incorrectly formatted. If you want, I could take a quick look at them. ...
written 11 weeks ago by Maxime Lamontagne1.9k
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Comment: C: Using Plink, get allele frequencies for a subset of individuals
... Try this : ./plink --file /path/in_data --chr 1-22 --allow-extra-chr --keep NewFile.txt --make-bed --out Temp1 --allow-no-sex ./plink --bfile Temp1 --pheno /path/cases.txt --freq --out out_data_case --allow-no-sex ...
written 11 weeks ago by Maxime Lamontagne1.9k
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Answer: A: Using Plink, get allele frequencies for a subset of individuals
... Create a file with only the FID and IID of the subjects you want to keep (NewFile.txt). Then try this : ./plink --file /path/in_data --chr 1-22 --allow-extra-chr --keep NewFile.txt --pheno /path/cases.txt --freq --make-bed --out out_data_case ...
written 11 weeks ago by Maxime Lamontagne1.9k
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Answer: A: Convert SNPs from GrCh38 to 37
... Try UCSC LiftOver : https://genome.ucsc.edu/cgi-bin/hgLiftOver ...
written 3 months ago by Maxime Lamontagne1.9k
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Answer: A: How to get a unique target gene for each SNP from different chromosomes/genes in
... Try ANNOVAR (table_annovar.pl) : [http://annovar.openbioinformatics.org/en/latest/user-guide/startup/][1] [1]: http://annovar.openbioinformatics.org/en/latest/user-guide/startup/ ...
written 4 months ago by Maxime Lamontagne1.9k

Latest awards to Maxime Lamontagne

Appreciated 27 days ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Good Answer 27 days ago, created an answer that was upvoted at least 5 times. For A: Accounting for problem SNPS when merging multiple plink files
Scholar 27 days ago, created an answer that has been accepted. For A: Plink MAF Calculation
Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Scholar 4 months ago, created an answer that has been accepted. For A: Plink MAF Calculation
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Commentator 8 months 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 8 months ago, created an answer that was upvoted at least 5 times. For A: Minor allele frequency calculation
Appreciated 9 months ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Appreciated 15 months ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Popular Question 15 months ago, created a question with more than 1,000 views. For How To Get Articles For A Snps List?
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Popular Question 18 months ago, created a question with more than 1,000 views. For Plotting Human Karyotype - Software
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Appreciated 22 months ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Minor allele frequency calculation
Epic Question 2.2 years ago, created a question with more than 10,000 views. For Bioinformatic Cartoon
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Post-Doctoral - Genomic Research Program On Cardio-Respiratory Diseases - Quebec City
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Plotting Human Karyotype - Software
Scholar 2.4 years ago, created an answer that has been accepted. For A: Plink MAF Calculation
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Plotting Human Karyotype - Software

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