User: lilingjoyo

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lilingjoyo30
Reputation:
30
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New User
Location:
Japan
Last seen:
1 year, 3 months ago
Joined:
5 years ago
Email:
l*********@163.com

Posts by lilingjoyo

<prev • 18 results • page 1 of 2 • next >
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why some genotyped snps are lost after imputation
... Hallo everyone, I'm using IMPUTE2 for genotype data phasing and imputing. But I found that lots genotyped variants are lost after imputation. Anyone had same phenomenon before? Do you know the reason? Any idea is welcomed. ...
genotype imute2 written 15 months ago by lilingjoyo30
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how to study genetic correlation between two traits
... Hi all, I have summary statistic table of trait A and genotype data of trait B. I want to study genetic correlation between trait A and trait B. Lots papers about this kind of topics have been published, most of them use LD score regression which take summary statistic table as input. But I want to ...
genetic correlations gwas genotype written 18 months ago by lilingjoyo30 • updated 18 months ago by genomax91k
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Comment: A: Why there is no beta of SE output in some meta GWAS results?
... Sorry, spelling mistake. Yeah, it's METAL. ...
written 18 months ago by lilingjoyo30
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Why there is no beta of SE output in some meta GWAS results?
... Hi all, I want to use a summary statistics of a meta GWAS result. The meta analysis was performed by using META. In the summary statistic table, there are z-score and p-value columns, but no beta or SE columns. But I need beta as my input. Here is header of the summary table SNP CHR BP Allele1 ...
gwas meta beta se written 18 months ago by lilingjoyo30
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Comment: C: the lower unique mapping rate after Trimming
... Hi genomax, thanks. That's also what I thought. I think unique mapping rate is top priority for accessing the data quality. If this is higher without trimming, then I just pass the trimming process. If things go wring during mapping, then I will trace back and check it. ...
written 23 months ago by lilingjoyo30
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Comment: C: the lower unique mapping rate after Trimming
... Thanks genomax. Can you make it more clear wether or not I need to do trimming based on current condition. The *% of reads mapped to multiple loci* is higher, but the *Uniquely mapped reads %* is higher too in sample without trimming. It's unreasonable. ...
written 23 months ago by lilingjoyo30
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Comment: A: the lower unique mapping rate after Trimming
... If the mapping result of trimmed data is worse, is it necessary to do trimming? ...
written 23 months ago by lilingjoyo30
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the lower unique mapping rate after Trimming
... Hallo everone, I came into some tricky problems with processing total stranded RNA-seq data. I used trimmomatic tool to trim adapter sequence and low quality reads. Then, used STAR to map the clean reads to GRCh38. But the unique mapping rate is quite poor than my colleague's who just use the raw ...
trimmomatic star rna-seq written 23 months ago by lilingjoyo30
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genomic inflation factor calculation
... hallo, everyone. I'm new to GWAS data analysis. When I do QQ plot for my association analysis result produced by snptest software. The observed p-value is deviated from expected p-value. But the inflation factor lambda is quite small, it's only 1.03. How to explain this phenomenon. Followings are ...
gwas qq plot inflation factor written 2.4 years ago by lilingjoyo30
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how to convert top/bot, or plus/minus strand to positive/negative strand
... I‘m trying to convert top/bot or plus/minus strand of Illumina genotype array to positive strand of reference genome. Because I want to do imputation which requires my genotype is based on positive strand. Name SNP ILMN Strand Customer Strand 1:100292476 [A/G] TOP TOP 1:101064936 [A/G] ...
genome written 2.5 years ago by lilingjoyo30 • updated 2.5 years ago by WouterDeCoster44k

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Popular Question 17 months ago, created a question with more than 1,000 views. For methods of integrating microarray data and RNAseq data
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