User: Cindy

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Cindy10
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Posts by Cindy

<prev • 5 results • page 1 of 1 • next >
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How does FastQTL deal with strand
... FastQTL phenotype.bed input does not have strand column as in QTLtools. How does the software deal with strand? I guess a related question would be say gene1 is on the reverse/minus strand in GTF file. Should its end position in GTF file be the TSS (transcription start site) for fastQTL phenotype.b ...
qtl rna-seq written 4 months ago by Cindy10 • updated 8 weeks ago by Biostar ♦♦ 20
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fastQTL phenotypes with no cis-variants
... Hi, I've been using FastQTL to map cis-QTL for molecular phenotypes. Correct me if I'm wrong, but I just noticed that nominal pass is not outputting phenotypes without any variants in cis-window, while permutation pass is indeed outputting these phenotypes, with 0 in the number_of_variants column an ...
qtl rna-seq written 4 months ago by Cindy10
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How does salmon deal with decoy?
... I'm using Salmon's selective alignment mode (--validateMappings) with decoy-aware index generated from gencode.transcriptome.fa and decoys.txt. I want to make sure that salmon does not output quantifications for these decoy sequences, correct? These decoy sequences begin with "GL....". They are jus ...
salmon rna rna-seq written 5 months ago by Cindy10 • updated 5 months ago by Rob4.6k
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Comment: C: How is vcf-merge handling different INFO for a single variant?
... Thank you! Exactly what I was looking for. I just want to confirm vcf-merge is following the same default, getting INFO from the first input file. I couldn't find it in the vcftools documentation. ...
written 7 months ago by Cindy10
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How is vcf-merge handling different INFO for a single variant?
... I imputed several different datasets with the Michigan imputation server and downloaded the output dose.vcf.gz files. I then merged them together by chromosome. I have used both vcf-merge and bcftools merge. My question is, for the same variant, r-square imputation quality can be different between d ...
bcftools vcfools imputation rna-seq written 7 months ago by Cindy10

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