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 ...
tophat2 ngs alignment hisat2 written 3 months ago by veronicaschroeder78100
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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 6 months 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 7 months ago by veronicaschroeder78100
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Comment: C: Affymetrix microarrays parsing
... Exactly which fields of the txt file you need to extract? ...
written 7 months 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 7 months 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 7 months 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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Great Question 12 months ago, created a question with more than 5,000 views. For List Of File Formats Used In Bioinformatics?
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