User: moxu

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moxu440
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Posts by moxu

<prev • 215 results • page 1 of 22 • next >
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How to build an imputation reference panel from a fasta file of many samples
... I have a fasta file for dozens of thousands of human mitochondrial genome sequences (aligned already) in fasta format. I want to construct a reference panel using these samples to impute genotyped samples, but I don't know how to do so properly. BTW, anyone has thought about how to impute mtDNA mar ...
assembly alignment snp sequencing written 4 weeks ago by moxu440
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Comment: C: How to plot haplogroup map with pie charts?
... Have you found a solution? Given a haplogroup, how do you find our the geographic information associated with the haplogroup? ...
written 11 weeks ago by moxu440
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Comment: C: Y-DNA and mtDNA Haplogroup Predictor
... Thanks so much for the reply. How about MToolBox? ...
written 12 weeks ago by moxu440
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Answer: A: Y-DNA and mtDNA Haplogroup Predictor
... I am looking for a good haplogroup classifier using either genotyped information (SNPs) or WGS information (sequencing). Which software products are the most popular (and accurate)? Thanks! ...
written 12 weeks ago by moxu440
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Comment: A: Plot local ancestry on chromosome
... Any luck? It looks like Martin's approach is outdated. ...
written 6 months ago by moxu440
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Comment: C: How plink calculates the INFO scores ?
... Have you got an answer? ...
written 8 months ago by moxu440
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Answer: A: How to convert Merlin phased result files to vcf
... The answer is that mega2 cannot take Merlin's .chr/.flow as input and cannot convert them to .vcf. The suggestion I got from the mega2 professor is to use shapeit, which can do trio phasing and can convert to vcf. ...
written 10 months ago by moxu440
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How to convert Merlin phased result files to vcf
... I used Merlin to do family trio phasing. Merlin generated a .chr file and a .flow file for each chromosome. I need to convert these files to .vcf files, or at least to a format that is more modern and popular. Any suggestions/recommendations would be highly appreciated. ...
genome assembly snp software error written 10 months ago by moxu440
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How to resolve kinship with the software "king" using GWAS genotyping data?
... "king" can impute IBS0 and kinship coefficient using GWAS samples. It can generate Z0 (probability of IBD0) for within-family members but this is not common for a GWAS population. So how can you resolve the kinship using the king output file? For instance, how can you tell parent-child, monozygotic ...
snp written 11 months ago by moxu440
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Comment: C: How Do You Justify Your Rna-Seq Expression Threshold (Fpkm/Rpkm) ?
... We used RSEM to align and quantify the RNA-seq levels, and use estimated gene count = 5 as the threshold -- if none of the samples has gene count >= 5, that gene is filtered out and not used for downstream analysis. Unless you have a strong reason not to do so, this filtering method should serve ...
written 12 months ago by moxu440

Latest awards to moxu

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