User: Phoenix Mu

gravatar for Phoenix Mu
Phoenix Mu40
Reputation:
40
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New User
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Last seen:
1 month ago
Joined:
2 years, 3 months ago
Email:
m*******@gmail.com

Posts by Phoenix Mu

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Empty output of allele specific expression analysis by GATK
... Did you make sure that your sample names in VCF file can be found as Read group in BAM file? ...
written 4 weeks ago by Phoenix Mu40
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Answer: A: Bedtools Genomecoveragebed Usage : How To Create A Genome File?
... I think this answer might be helpful although I am late. I saw this from the help page of `genomeCoverageBed`: Tips: One can use the UCSC Genome Browser's MySQL database to extract chromosome sizes. For example, H. sapiens: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \ "sele ...
written 13 months ago by Phoenix Mu40
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Answer: A: Plots using GWAS and eQTL datasets with locuszoom
... I think for Figure 2 in the paper you linked, it cannot be done by LocusZoom. The author did not do that, obviously. ...
written 19 months ago by Phoenix Mu40
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Comment: A: Illumina genotyping report to Plink files
... Does segmentation error typically mean that there is not enough memory? ...
written 20 months ago by Phoenix Mu40
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Michigan imputation server quality control failed
... I am using Michigan Imputation Server. I have performed a initial QC and removed monomorphic sites and sites with MAF > 0.5. However, the QC step on the server failed. There is no error message or logfile that I can check. So I just do not know how to find out what is wrong with my VCF file. ...
imputation genotype written 20 months ago by Phoenix Mu40
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Answer: A: Change sample names in vcf
... It seems that `bcftools reheader --samples -o ` would be helpful. ...
written 20 months ago by Phoenix Mu40
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Answer: A: How to overlay qq plots
... This is the function I used. It is modified from the original `qq()` function from `qqman` package. qqplot <- function(pvector, col = "black", add = F, ylim = NULL){ expectedP <- -log10(ppoints(length(pvector))) observedP <- -log10(sort(pvector, decreasing = F)) if (a ...
written 21 months ago by Phoenix Mu40
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Comment: C: FastQTL - GNU Scientific Library (GSL) Domain Error
... This solution is really helpful. I was running using filtered data, but then I used all the coding genes and got this error, so I think that this has something to do with lowly expressed data. However, maybe you could try nominal option instead of permutation. ...
written 22 months ago by Phoenix Mu40
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Flipped Ref allele in VCF file
... I am doing an eQTL mapping analysis. After getting my results, I can plot the slope from regression with normalized expression together to visualize the results. But I found something that is really wired when doing this. ![enter image description here][1] ![enter image description here][2] As yo ...
vcf plink snp written 22 months ago by Phoenix Mu40
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Comment: C: Duplicate ID in bed file
... Right, I think `--list-duplicate-vars` only find SNPs duplicated by position. ...
written 22 months ago by Phoenix Mu40

Latest awards to Phoenix Mu

Popular Question 11 months ago, created a question with more than 1,000 views. For Normalize and filter RNA-seq data
Popular Question 17 months ago, created a question with more than 1,000 views. For Does .sra.cache file means failed download?
Popular Question 17 months ago, created a question with more than 1,000 views. For Insignificant QQ plot in GWAS

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