User: rkostadi

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rkostadi60
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Posts by rkostadi

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Calculating Coverage Using CIGAR String
... Why don't you remove `vector lens` and instead have `int total=0;` and `total+=it->Length()` inside the loop and `cov = total*1.0/(end-start+1)`? ...
written 19 months ago by rkostadi60
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Answer: A: Which Application Is Truly Missing In Bioinformatics?
... I am looking for one that gives me the answer to life, the universe and everything. I guess something like echo "42". Killer apps need killer problems to solve. ...
written 2.0 years ago by rkostadi60
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Answer: A: considerations for epiallele studies (DNA methylation Bisulfite Sequencing)
... Who is they? Can you provide a reference? There's no reason to exclude longer CpG methylation haplotypes from the analyses. I consider 5- and 6- long ones too. Average CpG to neighboring CpG distance is about 100bp, median is about 40bp for the human genome, that's why with paired end sequencing you ...
written 2.0 years ago by rkostadi60
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Answer: A: Highly Variable SNP
... Data from the 1k human genomes has ALT allele frequencies. I would download it from: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html And, then select biallelic SNPs with high frequency of ALT allele (columns 6-10). ...
written 2.1 years ago by rkostadi60
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Comment: C: What is the most suitable file format for storing sequence alignments and associ
... If you have assembled each genome from reads, so that you have one sequence string per genome, and you have performed multiple sequence alignment on all assembled genomes, then the nexus format is best suited for downstream purposes, such as tree inference and annotation correlations. However, from ...
written 2.2 years ago by rkostadi60
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Answer: A: Comparing WGS, WXS, and SNP Array data
... The key is to get the break points right. See if the 3 segmented wgs wxs array profiles get the same or different break points for CN events. Segmentation is art. Also, all 3 platforms will give you allelic imbalance information, use it. Evaluate # of events called by 1,2,3, concordance in break po ...
written 2.2 years ago by rkostadi60
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Answer: A: parsing fasta file
... fold -w 60 input.fa ...
written 2.2 years ago by rkostadi60

Latest awards to rkostadi

Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Calculating Coverage Using CIGAR String

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