User: Apprentice

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Apprentice40
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Posts by Apprentice

<prev • 59 results • page 1 of 6 • next >
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Detection of excess IBD segments in patients
... Hi. I have SNP array data for 10 case and 100 control subjects. I think that the case subjects have local shared IBD segments on chromosome 10. So, I would like to detect excess IBD segments in case subjects. I could identify shared IBD segments in each pair of the all subjects using SHAPEIT2 and ...
ibd sgements snp written 1 day ago by Apprentice40
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Calculation of frequency of each haplotype from .hap file
... Hi. I have SNP data set phased by SHAPEIT2. The file is saved in the .hap format. I would like to calculate frequency of each haplotype from the .hap file in each group of case and controls. Could you tell me what software can calculate the frequency of each haplotype from the .hap file? ...
haplotype snp written 5 days ago by Apprentice40
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Definition of + and - strands for human genome
... Hi. As you know, UCSC genome browser named two DNA strands of human genome "+" and "-" strands. I would like to know how one of the two DNA strands was defined as a + strand and the other was defined as a - strand. Could you tell me the definitions of + and - strands? ...
genome written 10 weeks ago by Apprentice40
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Comment: C: How to calculate covariance between betas for GxE interaction using PLINK 2.0
... Thank you for your quick response. I got it. ...
written 3 months ago by Apprentice40
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How to calculate covariance between betas for GxE interaction using PLINK 2.0
... Hi. I would like to perform genome-wide meta-analysis of GxE interaction across 5 cohorts. I'm going to use a joint meta-analysis of Mannig et al. (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3312394/) I know that the method needs SNP beta and SNP×E beta and covariance between the betas. I coul ...
interaction snp written 3 months ago by Apprentice40 • updated 3 months ago by chrchang5237.3k
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Imputation of X chromosome non-PAR for male subjects
... Hi. I did an imputation of X chromosome SNPs for male subjects by using Minimac3. I got a vcf file of the imputed SNPs. The males on the non-pseudoautosomal part of the X chromosome were coded as 0 or 1. However, I hope that males on the non-pseudoautosomal part of the X chromosome were coded as ...
imputation snp x chromsoome written 12 months ago by Apprentice40
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Comment: C: How to trim poly-sequence before or after trimming by Trimmomatic.
... Thank you for your reply. I'll try to use the solution from ATpoint. ...
written 12 months ago by Apprentice40
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Comment: C: How to trim poly-sequence before or after trimming by Trimmomatic.
... Thank you for your advice. ...
written 12 months ago by Apprentice40
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Comment: C: How to trim poly-sequence before or after trimming by Trimmomatic.
... I would like to remove polyA tails using prinseq. My RNA-seq data is paired end. My fastq files were gzipped. It seems that prinseq can't read gzipped fastq files. I don't want to decompress the fastq files. Could you tell me how to use prinseq for paired-end gzipped fastq files? ...
written 12 months ago by Apprentice40
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Comment: C: How to trim poly-sequence before or after trimming by Trimmomatic.
... Thank you for your advice. I'll try it. ...
written 12 months ago by Apprentice40

Latest awards to Apprentice

Popular Question 13 months ago, created a question with more than 1,000 views. For Software For Hiseq/Pacbio Hybrid Assembly In Human Genome
Popular Question 15 months ago, created a question with more than 1,000 views. For Software For Hiseq/Pacbio Hybrid Assembly In Human Genome
Popular Question 15 months ago, created a question with more than 1,000 views. For How to merge two vcf files, which have same variants but don't regard same variants
Popular Question 15 months ago, created a question with more than 1,000 views. For Software For Hiseq/Pacbio Hybrid Assembly In Human Genome
Popular Question 22 months ago, created a question with more than 1,000 views. For Software For Hiseq/Pacbio Hybrid Assembly In Human Genome
Popular Question 22 months ago, created a question with more than 1,000 views. For Can GATK read compressed vcf files?
Popular Question 22 months ago, created a question with more than 1,000 views. For Method to merge two vcf files that don't have same alt information
Popular Question 2.1 years ago, created a question with more than 1,000 views. For How to merge two vcf files, which have same variants but don't regard same variants
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Can GATK read compressed vcf files?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How to merge two vcf files, which have same variants but don't regard same variants
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Can GATK read compressed vcf files?

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