User: Maxime Lamontagne

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Posts by Maxime Lamontagne

<prev • 138 results • page 1 of 14 • next >
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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 24 days 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 4 weeks ago by Maxime Lamontagne1.8k • updated 4 weeks ago by WouterDeCoster19k
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Answer: A: Merge ped files in PLINK
... Try the merge option : https://www.cog-genomics.org/plink2/data#merge ...
written 4 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 4 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 4 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 4 months 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 4 months 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 4 months 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 10 months ago by Maxime Lamontagne1.8k • updated 10 months ago by genomax29k
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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 11 months ago by Maxime Lamontagne1.8k

Latest awards to Maxime Lamontagne

Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Snp Information From Ped File In Plink
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