User: lilingjoyo

gravatar for lilingjoyo
lilingjoyo30
Reputation:
30
Status:
New User
Location:
Japan
Last seen:
1 week, 1 day ago
Joined:
3 years, 7 months ago
Email:
l*********@163.com

Posts by lilingjoyo

<prev • 17 results • page 1 of 2 • next >
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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 5 weeks ago by lilingjoyo30 • updated 5 weeks ago by genomax67k
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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 7 weeks 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 7 weeks 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 5 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 5 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 5 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 5 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 11 months 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 12 months ago by lilingjoyo30 • updated 12 months ago by WouterDeCoster39k
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Comment: C: strange htseq-count result
... In fact, I tried both. They put almost same result. All reads are in "no feature" or "ambiguous" group. ...
written 13 months ago by lilingjoyo30

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Popular Question 12 months ago, created a question with more than 1,000 views. For methods of integrating microarray data and RNAseq data
Popular Question 3.5 years ago, created a question with more than 1,000 views. For methods of integrating microarray data and RNAseq data
Popular Question 3.5 years ago, created a question with more than 1,000 views. For TCGA somatic mutation
Popular Question 3.5 years ago, created a question with more than 1,000 views. For edegR, export TMM normalized method

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