User: anamaria

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anamaria80
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Posts by anamaria

<prev • 69 results • page 1 of 7 • next >
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How to reduce number of entries in QQ plot?
... Hi, I made this QQ plot via: selecting p values <0.001 from my data set which has in total has 5556249 points. After taking only P<0.001 I get 3713, and I plot it: library(qqman) dd=df[df$P<1e-3,] qq(dd$P, main = "Q-Q plot of small GWAS p-values") and I get the attached plot ...
qq written 4 weeks ago by anamaria80
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Comment: C: What is the best tool for doing Quality Control checks on my raw RNA-seq data?
... Thank you so much for this very valuable feedback! ...
written 4 weeks ago by anamaria80
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Comment: C: What is the best tool for doing Quality Control checks on my raw RNA-seq data?
... thank you so much, for the actual analysis, after QC is done, would you recommend doing this: 1.Mapping/Alignment (in HISAT2), 2. Assign aligned reads to genes (in HTseq), 3.Differential expression (in DESeq2) ...
written 4 weeks ago by anamaria80
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What is the best tool for doing Quality Control checks on my raw RNA-seq data?
... Hello, I just got my Illumina RNA sequencing experiment results in fastq format. What would be the best software to do QC on this data? Can you please share some good tutorials on this subject? Thanks Ana ...
qc rna-seq fastqc written 4 weeks ago by anamaria80 • updated 4 weeks ago by adam.faranda80
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How to calculate TPR, true positive rate,for tissue sharing between two different tissues?
... Hello, I have to calculate sharing of EQTLs between two different tissues (retina and LCL), π1 statistic. Can you please point me to the methodology on this issue? I tried using qvalue function: library(qvalue) qval_obj=qvalue(pvalR) pi1=1-qval_obj$pi0 but after running: qval_ob ...
tpr written 12 weeks ago by anamaria80
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How to format plink2 pheno file?
... Hello, I was running this command: plink2 --threads 40 --vcf VCFchr22.vcf.gz --pheno pheno_Mtt.txt --pheno-name pheno --glm --out FINchr22 where my pheno_Mtt.txt looks like this (space separated): FID IID pheno 1 1000017 1000017 -9 2 1000025 1000025 -9 3 1000 ...
plink2 written 4 months ago by anamaria80
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Comment: C: Hwo to do quality control steps on UKBiobank data?
... Hi, yes I agree, and I mentioned above those 4 QC steps I plan to do. My question is more how to do this in Plink2? or some other software? For example to deal with MAF I would do this: plink2 --bgen ukb_imp_chr17_v3.bgen ref-first --sample ukb44316_imp_chr17_v3_s487317.sample --maf 0.001 ...
written 4 months ago by anamaria80
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Hwo to do quality control steps on UKBiobank data?
... Hello, I downloaded imputed .bgen and .sample files from UKBiobank and now I am planning to do GWAS in it. I plan to use Plink2. can you please tell me which QC steps I would have to perform? I was thinking to do these: -remove related individuals -remove non EUR -remove SNPs with ...
ukbiobank written 4 months ago by anamaria80
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What to do with the output of apt-geno-qc?
... Hello, I was running QC step on my .CEL files via: apt-geno-qc \ --cdf-file BI_SNP.cdf \ --qcc-file BI_SNP_1.qcc \ --qca-file BI_SNP.qca \ --cel-files cell.txt \ --dm-out outDM1 \ --out-file qc1.txt And my qc1.txt file looks like this: #%guid ...
affymetrix written 4 months ago by anamaria80
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Comment: C: What software to use to asses phenotypic information from ULBiobank dataset?
... Hi Ken, can you please explain what did you mean with: filter(icd10codes, str_detect(code, "E13")) what is code in this example? What I want to do is to extract from my dataset cases which comply with these 2 definitions: Data-Field 41270: E10.3,E11.3,E14.3,H360 + Data-Field 6148: Diabetes ...
written 4 months ago by anamaria80

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