User: Maxime Lamontagne

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

<prev • 142 results • page 1 of 15 • next >
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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 19 days ago by Maxime Lamontagne1.8k
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Answer: A: ANNOVAR - column description
... I found the meaning of these columns by downloading a Readme file from ExAC : > The loss-of-function Z score is highly correlated with gene length (r > = 0.57). This means that longer genes have higher (more intolerant) scores simply because we are more confident in their predictions. To > ...
written 19 days ago by Maxime Lamontagne1.8k
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ANNOVAR - column description
... Hi, I used ANNOVAR to annotate 1000 SNPs for a study. I've run the table_annovar.pl pipeline in the Quick Start-Up Guide page (http://annovar.openbioinformatics.org/en/latest/user-guide/startup/). In the output, I do not understand some columns and I can't find this information (pLi, pRec, pNul ...
annovar written 26 days ago by Maxime Lamontagne1.8k
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Answer: A: Feasible Annotation of 4 million unique SNPs
... I think ANNOVAR (http://annovar.openbioinformatics.org/en/latest/) could be useful. ...
written 5 weeks ago by Maxime Lamontagne1.8k
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Answer: A: How to make bed file for existing bim and fam file
... Use plink with the --merge-list option. plink --bfile Input-chr1 --merge-list List.txt --make-bed --out New-Output List.txt : > Input-chr2.bed Input-chr2.bim Input-chr2.fam > Input-chr3.bed Input-chr3.bim Input-chr3.fam > ... ...
written 11 weeks ago by Maxime Lamontagne1.8k
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Answer: A: Grep Position List
... Why not use R with the merge command? data1 <- read.table("VCF File", header=F, sep="\t") data2 <- read.table("Position File", header=F, sep="\t") merge.results <- merge(data2, data1, by.x="V1", by.y="V2", all=F) write.table(merge.results, "VCF Subset", col.names ...
written 12 weeks ago by Maxime Lamontagne1.8k • updated 12 weeks ago by WouterDeCoster20k
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Answer: A: Merge ped files in PLINK
... Try the merge option : https://www.cog-genomics.org/plink2/data#merge ...
written 6 months 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 6 months 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 6 months 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 6 months ago by Maxime Lamontagne1.8k

Latest awards to Maxime Lamontagne

Scholar 19 days ago, created an answer that has been accepted. For A: Plink MAF Calculation
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Commentator 4 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 4 months ago, created an answer that was upvoted at least 5 times. For A: Minor allele frequency calculation
Appreciated 5 months ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Appreciated 11 months ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Popular Question 11 months ago, created a question with more than 1,000 views. For How To Get Articles For A Snps List?
Popular Question 12 months ago, created a question with more than 1,000 views. For How To Get Articles For A Snps List?
Popular Question 14 months ago, created a question with more than 1,000 views. For Plotting Human Karyotype - Software
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Appreciated 18 months ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: Minor allele frequency calculation
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Popular Question 23 months ago, created a question with more than 1,000 views. For Post-Doctoral - Genomic Research Program On Cardio-Respiratory Diseases - Quebec City
Teacher 24 months ago, created an answer with at least 3 up-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
Scholar 2.1 years ago, created an answer that has been accepted. For A: Plink MAF Calculation
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: Snp Information From Ped File In Plink
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Plotting Human Karyotype - Software
Centurion 2.4 years ago, created 100 posts.
Teacher 2.4 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
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Plotting Human Karyotype - Software

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