User: veronicaschroeder78

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Posts by veronicaschroeder78

<prev • 21 results • page 1 of 3 • next >
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Where are examples of Interspersed repeats?
... Interspersed repeats are often defined as repetitive sequences dispersed throughout the genome. However such definition (IMO) does not exclude Tandem Repeat Sequences. So I started to search for examples of such sequences. After checking many Bioinformatics and Genetics books, I found many exampl ...
ministatellite str repeats sequence written 4 weeks ago by veronicaschroeder78100
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Where is "inference" applied in Haplotype inference?
... Suppose I have the following sequences with SNPs in 4th and 9th columns: IND1 GATATTCGGA- IND2 GATGTTCTGAA IND3 GATATTCGGA- IND4 GATATTCGGAA IND5 GATGTTCTGAA IND6 GATGTTCTGAA Haplotypes from such sequences would be: AG- (2/6) GTA (3/6) AGA (1/6) So far so good ...
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What's the difference between Phased Haplotypes and Phased Genotypes?
... I read a lot of articles using both terms without enough context. Are "Phased Haplotypes" synonymous of "Phased Genotypes"? What's the difference between them? ...
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Does HaploView perform phasing?
... I have super newbie questions. As far as I understand HaploView can display a PED file containing formatted collection of unphased genotype data. But HaploView **does not** perform haplotype inference (or phasing). Then if I load unphased .PED .INFO files in HaploView, what's displayed in the tri ...
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Comment: C: pca in eigenstrat
... But they are the same algorithm? Did they just copypasted the EIGENSTRAT algorithm in PLINK? ...
written 9 weeks ago by veronicaschroeder78100
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Comment: C: Affymetrix microarrays parsing
... Exactly which fields of the txt file you need to extract? ...
written 9 weeks ago by veronicaschroeder78100
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Comment: C: Plotting Linkage Disequilibrium Decay Across The Genome
... In R version 3.3.2 (2016-10-31) the line > ggplot(ld) + geom_line(aes(x=BP_B - BP_A, y = R2)) gives > Error in eval(expr, envir, enclos) : object 'BP_B' not found ...
written 10 weeks ago by veronicaschroeder78100
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Comment: C: How to convert input files from PLINK to snp.plotter?
... Now that's a better answer :). I am not doing any association since I don't have traits (at least yet, I don't do experiment design). I am exploring if snp.plotter visualizations could be nice alternative to HaploView and other haplotype visualization packages. As far as I can see, the mandatory S ...
written 10 weeks ago by veronicaschroeder78100
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From PHASE to HaploView
... I finally built a PHASE input file (.inp) and my analysis was executed successfully. Now I have phased output which consists of several files: - test4.out_freqs : haplotype frequency estimates - test4.out_pairs : most likely haplotype pairs for each individual - test4.out_recom : estimates of r ...
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Comment: C: How to convert input files from PLINK to snp.plotter?
... You are free to call stupid to anyone, but my question is about how to interpret the data they ask for the input file (my questions are pretty clear IMHO). The documentation says the PALETTE file is optional, they don't say anything optional about the GENOTYPE file. > A dataset is composed a c ...
written 10 weeks ago by veronicaschroeder78100

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Great Question 7 months ago, created a question with more than 5,000 views. For List Of File Formats Used In Bioinformatics?
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