User: Rubal7

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Rubal7720
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Posts by Rubal7

<prev • 75 results • page 1 of 8 • next >
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Comment: C: Functional Relevance Of Stop Retained Variants?
... Could you expand a little on what you mean, I am a little unclear how a synonymous change in a stop codon can be classified as a regulatory region? Thanks very much, probably just my confusion ...
written 4.7 years ago by Rubal7720
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Functional Relevance Of Stop Retained Variants?
... Hello Everyone, I am looking for functional variants in population genomic data. I have identified a candidate variant (high frequency and highly conserved across mammals). The variant is classified by VEP as a stop retained variant, meaning that "A sequence variant where at least one base in the t ...
genome variation disease functional genomics written 4.7 years ago by Rubal7720 • updated 4.7 years ago by Emily_Ensembl16k
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Answer: A: A Database Of Signatures Of Selection In The 1000 Genomes Dataset
... Great resource! ...
written 4.7 years ago by Rubal7720
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How To Identify If Gene Overlaps Between Studies Are Significant?
... Hello Everyone, I have a theoretical and methodological question and I would appreciate peoples ideas. We have run two independent studies (different species) to identify if similar genes are involved in a phenotype. From each species we have a list of candidate genes. Some of these genes overlap b ...
overlap gene written 4.7 years ago by Rubal7720 • updated 4.7 years ago by Istvan Albert ♦♦ 78k
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Comment: C: Pca From Vcf Files
... This sounds great ...
written 4.7 years ago by Rubal7720
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Comment: C: Most Appropriate Software Detect Population Specific Structural Variation In Mul
... Thanks for the reply. Low is 4x coverage per sample. Essentially this is a scan for variants of all sizes as we are looking at cases and controls. From a rough and ready look at read depth variation between the populations we see signs of some large duplications ~100-500kb and it would be good to se ...
written 5.3 years ago by Rubal7720
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Most Appropriate Software Detect Population Specific Structural Variation In Multiple Low-Coverage Genomes?
... Hello Everyone, I am looking for some advice on which software would be most suitable for detecting structural variation (particularly deletions and duplications > 100kb) that are fixed or at high frequency between two populations. I have low coverage sequence data (4x per sample) from 40 indivi ...
copynumber written 5.3 years ago by Rubal7720 • updated 4.6 years ago by Biostar ♦♦ 20
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Comment: C: R: Manhattan Plot Of Fst Values Instead Of -Log(P)
... Hi, I tried this code for data in the same format as above, am I missing something or should these two R commands be sufficient for plotting? Error in plot.window(...) : need finite 'xlim' values. Thanks ...
written 5.5 years ago by Rubal7720
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Comment: C: How To Perform A Fst (Fixation Index) Calculation Over A Vcf File Using A Slidin
... this is great, thanks for pointing it out! ...
written 5.6 years ago by Rubal7720
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How To Perform A Fst (Fixation Index) Calculation Over A Vcf File Using A Sliding Window?
... Hello Everyone, I have 2 vcf files, each one contains snps from samples from a single different population. I would like to run fst in windows along the genome to compare the populations. I am familiar with using vcf tools and therefore would like to run their weir-fst option. However currently thi ...
vcf vcftools written 5.6 years ago by Rubal7720 • updated 4.7 years ago by Biostar ♦♦ 20

Latest awards to Rubal7

Supporter 4.7 years ago, voted at least 25 times.
Student 6.3 years ago, asked a question with at least 3 up-votes. For What Are These Rp11 'Genes' In The Genome?
Popular Question 6.3 years ago, created a question with more than 1,000 views. For What Are These Rp11 'Genes' In The Genome?
Popular Question 6.5 years ago, created a question with more than 1,000 views. For Retrieve Subset Positions Vcf File
Popular Question 6.5 years ago, created a question with more than 1,000 views. For Comparing And Plotting Coverage Between Two Bam Files
Popular Question 6.5 years ago, created a question with more than 1,000 views. For Extract Sub-Set Of Regions From Vcf File
Popular Question 6.6 years ago, created a question with more than 1,000 views. For Pca From Vcf Files
Good Question 6.6 years ago, asked a question that was upvoted at least 5 times. For Pca From Vcf Files
Appreciated 6.6 years ago, created a post with more than 5 votes. For Pca From Vcf Files
Student 6.6 years ago, asked a question with at least 3 up-votes. For Pca From Vcf Files

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