User: veronicaschroeder78

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Posts by veronicaschroeder78

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Hisat2 warning: skipping mate
... I am a newbie in NGS data analysis and trying to run hisat2 after successfully building a index, with the following bash script: trimmedfiles=... (list of trimmed files from cutadapt) pairedfiles=... (list of trimmed files from cutadapt) hisat2 -t \ -p 8 \ -x my_genome_idx_p ...
ngs alignment hisat2 written 20 months ago by veronicaschroeder78110 • updated 7 months ago by ATpoint14k
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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 23 months ago by veronicaschroeder78110
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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 ...
haplotyping haplotype phase inference phasing written 23 months ago by veronicaschroeder78110
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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? ...
haplotypes haploview genotypes phasing plink written 23 months ago by veronicaschroeder78110
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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 ...
haplotypes haploview phase phasing fastphase written 2.0 years ago by veronicaschroeder78110
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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 2.0 years ago by veronicaschroeder78110
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Comment: C: Affymetrix microarrays parsing
... Exactly which fields of the txt file you need to extract? ...
written 2.0 years ago by veronicaschroeder78110
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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 2.0 years ago by veronicaschroeder78110
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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 2.0 years ago by veronicaschroeder78110
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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 ...

Latest awards to veronicaschroeder78

Great Question 2.4 years ago, created a question with more than 5,000 views. For List Of File Formats Used In Bioinformatics?
Popular Question 6.4 years ago, created a question with more than 1,000 views. For List Of File Formats Used In Bioinformatics?
Student 6.4 years ago, asked a question with at least 3 up-votes. For List Of File Formats Used In Bioinformatics?

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