User: User 7754

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User 7754140
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140
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United Kingdom
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8 hours ago
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7 years, 1 month ago
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Posts by User 7754

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Understanding HiChIP data and interactions
... Hi, I am new to HiChIP data and I was wondering what is the best way to call interactions, using only reads within peaks, or using reads where at least one segment is a peak? I have seen both approaches for HiChIP so I am not sure which is the way to go. Any thoughts are very much appreciated. ...
hichip written 17 hours ago by User 7754140 • updated 4 hours ago by Devon Ryan82k
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Comment: C: Convert INDEL format for use in Annovar
... Great! this would work, thank you!! ...
written 23 months ago by User 7754140
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Comment: C: Convert INDEL format for use in Annovar
... Hi, thank you Igor for your reply, but I don't have a VCF file only a simple text file so I can't really use the utilities for VCF right? Maybe I can anyway? Thanks again ...
written 23 months ago by User 7754140
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Convert INDEL format for use in Annovar
... Hi, I have a tab delimited file with GWAS results and I am trying to annotate the variants using Annovar but my format for INDELS is different, and I get my indels split between the invalid_input, where I find these SNPs in my file: 1 63735 63735 CCTA C 1 251627 251627 ...
indel annovar insertion-deletion annotation written 23 months ago by User 7754140 • updated 23 months ago by igor6.5k
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IMPUTE2 reference allele: same as matrixEQTL?
... When a dosage file is used for eQTL analysis using matrixEQTL, and the dosage file is with respect to a specific allele (e.g. the allele outputted as reference in IMPUTE2), is this also the reference allele used for the effect size computed in matrixEQTL? Thanks! ...
matrixeqtl impute2 imputation snp written 2.2 years ago by User 7754140
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Comment: C: bedtools intersectBed and GRanges countOverlaps
... Thank you Alex! I understand now. Apart from the difference in 1 base for snps, also the last position of the region.bed range and the first position do not count as overlaps using bedtools. Something to keep in mind. Thank you ...
written 2.4 years ago by User 7754140
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bedtools intersectBed and GRanges countOverlaps
... Hi, I am generating overlaps using this command in bedtools: intersectBed -a snps.bed -b region.bed -wb And now I am trying to compare the same files using the R package GenomicRanges, countOverlaps(snps, region.bed, type=c("within"), but I am not getting the same results. In particular, it see ...
bedtools R genomicranges bed written 2.4 years ago by User 7754140 • updated 2.4 years ago by Alex Reynolds25k
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Software to run genetic association analysis between a phenotype and SNPs, conditional on the top SNP
... Dear experts, I was wondering whether there are any packages available to automatically run conditional analysis, meaning association of a trait and variants in a region (y ~ SNPs), conditional on the best variant from the primary analysis (y ~ SNPs + top SNP). If there are not, I will proceed fro ...
conditional analysis association snp phenotype written 2.4 years ago by User 7754140
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Comment: C: P-value for enrichment of ChIP-Seq peaks within a genomic annotation
... Thanks this helps, but I am still confused about what our k would be, if we consider the number of ChiP-Seq peaks: q=10450-1, m=100561, n=204652, k=204652? Also would it not be important to consider that more than one ChIP peak can overlap each chromatin state? ...
written 2.8 years ago by User 7754140
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Comment: C: P-value for enrichment of ChIP-Seq peaks within a genomic annotation
... Hi and thanks for the reply! I have, but I am not sure what I would use for the totals including the non-overlapping peaks and annotations, would this be correct? phyper(10450, 100561, 100561+204652, 204652-100561) ...
written 2.8 years ago by User 7754140

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Great Question 6 months ago, created a question with more than 5,000 views. For Plot Genes In R Under A Regional Manhattan Plot
Popular Question 6 months ago, created a question with more than 1,000 views. For P-value for enrichment of ChIP-Seq peaks within a genomic annotation
Popular Question 6 months ago, created a question with more than 1,000 views. For Definition of splicing eQTLs in RNA-Seq and arrays
Popular Question 6 months ago, created a question with more than 1,000 views. For Tools for alternative splicing of distant genes
Popular Question 6 months ago, created a question with more than 1,000 views. For Circos or circlize plot for overlapping values/colors
Popular Question 6 months ago, created a question with more than 1,000 views. For [SOLVED] Trying to apply overlap to each row of a "GRangesList"
Popular Question 10 months ago, created a question with more than 1,000 views. For P-value for enrichment of ChIP-Seq peaks within a genomic annotation
Popular Question 23 months ago, created a question with more than 1,000 views. For P-value for enrichment of ChIP-Seq peaks within a genomic annotation
Popular Question 23 months ago, created a question with more than 1,000 views. For Tools for alternative splicing of distant genes
Popular Question 23 months ago, created a question with more than 1,000 views. For Circos or circlize plot for overlapping values/colors
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Combined Association Of Expression, Genetic, Clinical Phenotypes
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Combined Association Of Expression, Genetic, Clinical Phenotypes
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Combined Association Of Expression, Genetic, Clinical Phenotypes
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Plot Genes In R Under A Regional Manhattan Plot
Commentator 3.7 years ago, created a comment with at least 3 up-votes. For C: Eqtl Database Available?
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Visualise Ld Plots On Whole Chromosome
Popular Question 6.1 years ago, created a question with more than 1,000 views. For Plot Genes In R Under A Regional Manhattan Plot

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