User: moushengxu

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moushengxu330
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Posts by moushengxu

<prev • 209 results • page 1 of 21 • next >
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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 5 weeks ago by moushengxu330
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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 6 weeks ago by moushengxu330
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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 10 weeks ago by moushengxu330
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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 3 months ago by moushengxu330
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Comment: C: Can someone please help me run any GATK4 pipeline?
... java -jar cromwell-31.jar run germline_single_sample_workflow.wdl --inputs germline_single_sample_workflow.hg38.inputs.json ...
written 3 months ago by moushengxu330 • updated 3 months ago by Ram17k
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Comment: C: Can someone please help me run any GATK4 pipeline?
... I noticed that. I ran it on my MacBook Pro (MacOS 10.13.4), which should be the supported filesystem "MacOSXFileSystem" Do I have to do anything as described at http://cromwell.readthedocs.io/en/develop/backends/HPC/#filesystems? ...
written 3 months ago by moushengxu330
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Can someone please help me run any GATK4 pipeline?
... GATK4 is a great variant calling software product and is dominating in the field. Unfortunately, I am not able to run any of the GATK4 pipelines, probably because these pipelines all use google storage which I am not familiar with? Now I am trying to run the $5 variant calling pipeline because I gue ...
software error next-gen snp sequencing written 3 months ago by moushengxu330 • updated 3 months ago by vdauwera810
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Comment: C: Where to find information on LD ~ distance?
... One more question: it looks like the they limited the distance between SNPs to be under 200kb, while at 200kb, there are still tons of significant LDs as the data can tell. I am not sure why they cut it off at 200kb and do not look beyond 200kb? ...
written 4 months ago by moushengxu330
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Comment: C: Where to find information on LD ~ distance?
... That is it! Thanks so much! ...
written 4 months ago by moushengxu330
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Where to find information on LD ~ distance?
... We want to know how far away Linkage Disequilibrium (LD) can go between SNPs, but I have difficulty locating such information. I checked out SNPsnap from Broad Institute at https://data.broadinstitute.org/mpg/snpsnap/database_download.html, but it actually does not have such information. Any help ...
genome snp written 4 months ago by moushengxu330

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Scholar 14 days ago, created an answer that has been accepted. For A: edgeR artifacts on p-value and/or fold change?
Scholar 5 weeks ago, created an answer that has been accepted. For A: edgeR artifacts on p-value and/or fold change?
Great Question 7 weeks ago, created a question with more than 5,000 views. For how to avoid R automatically converting strings to numbers
Popular Question 10 weeks ago, created a question with more than 1,000 views. For rsem-calculate-expression ran out of memory
Popular Question 11 weeks ago, created a question with more than 1,000 views. For How does edgeR do ERCC spike-in normalization?
Popular Question 5 months ago, created a question with more than 1,000 views. For Step by step instructions to phase with Eagle?
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Scholar 19 months ago, created an answer that has been accepted. For A: edgeR artifacts on p-value and/or fold change?
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