User: moushengxu

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moushengxu300
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Posts by moushengxu

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Comment: A: How To Create The .Legend And .Phase Files For Gwas Imputation When Using Mach
... Have you found a solution on this? I am having a hard time locating these files right now. Your help would be highly appreciated! Thanks a lot! ...
written 3 days ago by moushengxu300
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Comment: C: HapMap 3 phased haplotype
... How about the legend files used by MaCH (mach1)? I am having a hard time locating these files. Thanks a lot! ...
written 3 days ago by moushengxu300
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mach1 phasing reference Haplotypes file(s)
... mach1 has an option "-h" to specify reference haplotypes for phasing, but I am having trouble finding such a reference haplotypes file. I would like to use haplotype reference from the 1000 Genome project, and I have tried "-h mydir/ALL.chr20.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotyp ...
software error snp written 5 days ago by moushengxu300
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Comment: C: Run Time Of Imputation Using 1000 Genomes
... Just a quick question: what's the file format for the "chr1ref.hap" file in "–h chr1ref.hap"? Thanks! ...
written 5 days ago by moushengxu300
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Comment: C: Merlin format, Mach, Plink, Plink2, and best practices of snp imputation
... OK, thanks a lot for the clarification. I thought MaCH go hand-in-hand with Merlin. I don't mind writing my own scripts for little things like this, but if there is something free, it might be better. Very often, I found it more time consuming to search for small tools to do trivial tasks than writi ...
written 6 days ago by moushengxu300
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Comment: C: Merlin format, Mach, Plink, Plink2, and best practices of snp imputation
... We want to evaluate different phasing/imputation software products, MaCH is one of them. "mach1" is the only MaCH I can obtain now. Thanks a lot for the information about plink. Are you suggesting me to convert .ped to .bed and then use plink2 instead? ...
written 7 days ago by moushengxu300
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Merlin format, Mach, Plink, Plink2, and best practices of snp imputation
... I have been fighting with the different GWAS file formats recently, and getting confused more and more, so I would like to get some enlightenments from experienced users here. I took me a while to figure out that the plink .ped & .dat file formats are different from the Mach (& thus merlin? ...
software error snp written 7 days ago by moushengxu300
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Comment: C: How to map probeset associated statistics to gene statistics in microarray diffe
... I used geo2r offered by GEO DB, and it generates p-value, logFC, etc. Thanks! ...
written 7 weeks ago by moushengxu300
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How to map probeset associated statistics to gene statistics in microarray differential expression analysis?
... For microarray data, differential expression analysis is done for each probeset. The problem is that one gene is typically mapped to multiple probesets. Since for most if not all practical reasons, we are interested in differential expression at the gene but not probeset level, I am wondering what's ...
gene R rna-seq written 7 weeks ago by moushengxu300 • updated 7 weeks ago by Kevin Blighe17k
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Comment: C: rsem-prepare-reference and mouse mm9 genome reference files
... Why don't you just use a gtf? It makes sense to use a reference genome and it's easier that way. ...
written 7 weeks ago by moushengxu300

Latest awards to moushengxu

Popular Question 27 days ago, created a question with more than 1,000 views. For Step by step instructions to phase with Eagle?
Popular Question 28 days ago, created a question with more than 1,000 views. For Step by step instructions to phase with Eagle?
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Step by step instructions to phase with Eagle?
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Step by step instructions to phase with Eagle?
Popular Question 4 months ago, created a question with more than 1,000 views. For edgeR and GO analysis using goana
Scholar 5 months ago, created an answer that has been accepted. For A: edgeR artifacts on p-value and/or fold change?
Popular Question 7 months ago, created a question with more than 1,000 views. For t-test or linear regression?
Popular Question 7 months ago, created a question with more than 1,000 views. For edgeR and GO analysis using goana
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: SNPEFF for de novo transcriptome annotation
Popular Question 11 months ago, created a question with more than 1,000 views. For edgeR and GO analysis using goana
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Scholar 14 months ago, created an answer that has been accepted. For A: edgeR artifacts on p-value and/or fold change?
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