User: dec986

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dec986230
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Posts by dec986

<prev • 134 results • page 1 of 14 • next >
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Comment: C: How to extract sample IDs from VCF into new VCF?
... Indeed, this is the solution ...
written 1 day ago by dec986230
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How to extract sample IDs from VCF into new VCF?
... I've written a script that extracts VCF IDs from a large VCF, in order to get a subset of the sample IDs (people). This script copies the header from the original VCF and simply pastes it into the new one. I then extract only the sample IDs that I need for each line in the original VCF. However, I ...
vcf written 1 day ago by dec986230
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Comment: C: Can Plink 1.07 set-hh-missing output VCF?
... `~/Scripts/plink1.9/plink --vcf ZZQDBCZE.chrX.vcf.gz --set-hh-missing --out tmp --recode vcf` is the correct answer to my question ...
written 6 days ago by dec986230
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Comment: C: Can Plink 1.07 set-hh-missing output VCF?
... I kept seeing beta for Plink 1.9, which made me think that it's not ready ...
written 6 days ago by dec986230
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Can Plink 1.07 set-hh-missing output VCF?
... Hello, I'm running the command plink-1.07-x86_64/plink --file ZZQDBCZE.chrX.vcf.gz --make-bed --set-hh-missing --out tmp --noweb but this is outputting a bed file, which I can't use, as I need a VCF. I either need a way to convert this to tmp.bed to VCF, or a way for plink to output tmp.vcf. ...
plink written 6 days ago by dec986230 • updated 6 days ago by chrchang5237.1k
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Comment: C: Cannot find faToTwoBit download
... thank you!! danke schön!! ...
written 7 days ago by dec986230
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Cannot find faToTwoBit download
... I'm looking through the website http://hgdownload.soe.ucsc.edu and I cannot find the download for the Linux x86_64 faToTwoBit I downloaded twoBitToFa about a year and a half ago, but cannot find the reverse binary anywhere on the internet now. I see https://genome.ucsc.edu/goldenPath/help/twoBit ...
2bit fasta download written 7 days ago by dec986230 • updated 7 days ago by ATpoint36k
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How to create Survival Formula for Phenotype Data?
... Hello, I'm using survminer to try to create a survival formula for a phenotype data set. library("survival", "survminer") data <- read.csv(file = "Study.cleaned.csv", header = TRUE) basic.cox <- coxph(formula = Surv(Observation_time, Event_Detected) ~ Patient_Age + Sex+BMI, data ...
survival written 6 weeks ago by dec986230
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Comment: C: bcftools cannot switch alt and ref alleles, IDs missing
... unfortunately, this still keep things in gVCF format :( ...
written 5 months ago by dec986230
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Comment: C: bcftools cannot switch alt and ref alleles, IDs missing
... the chromosomes all match ...
written 5 months ago by dec986230

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For R programming: Keep Heatmap Items Within Image Frame
Great Question 11 weeks ago, created a question with more than 5,000 views. For Long Read Length, yet STAR says many reads too short
Great Question 5 months ago, created a question with more than 5,000 views. For Long Read Length, yet STAR says many reads too short
Popular Question 5 months ago, created a question with more than 1,000 views. For R programming: Keep Heatmap Items Within Image Frame
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Popular Question 14 months ago, created a question with more than 1,000 views. For R programming: Keep Heatmap Items Within Image Frame
Popular Question 14 months ago, created a question with more than 1,000 views. For Conversion between .bedGraph or .bw to 7-column format
Popular Question 14 months ago, created a question with more than 1,000 views. For Zero Counts for many genes in 1 replicate, why?
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Popular Question 16 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
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Popular Question 19 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 23 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 23 months ago, created a question with more than 1,000 views. For R programming: Keep Heatmap Items Within Image Frame
Popular Question 23 months ago, created a question with more than 1,000 views. For Conversion between .bedGraph or .bw to 7-column format
Popular Question 23 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
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