User: Raony Guimarães

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raonyguimaraes
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PhD in Bioinformatics with experience in developing software and methods to the fields of Precision Medicine and Pharmacogenomics.

Currently working for a company called Genomics Medicine Ireland developing Bioinformatics software for doing NGS analysis.

Posts by Raony Guimarães

<prev • 79 results • page 1 of 8 • next >
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Hi Kevin, Just a small typo, it's actually: `gunzip human_g1k_v37.fasta.gz ;` ...
written 3 days ago by Raony Guimarães1000
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Answer: A: BCL files as deliverables from a sequencing center
... > Is this something sequencing providers or core facilities usually give > their customers? No, this is not very common but I can understand why someone would ask for that. (i.e. They prefer to do sample demultiplexing themselves adjusting the penalty parameters or use a different software ra ...
written 3 months ago by Raony Guimarães1000 • updated 3 months ago by ATpoint21k
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Comment: C: How to create 1000G_phase1.snps.high_confidence.hg19.sites.vcf ?
... Here you find an explanation about what makes it having high confidence: https://media.nature.com/original/nature-assets/nature/journal/v491/n7422/extref/nature11632-s1.pdf It was a combination of multiple strategies. ...
written 5 months ago by Raony Guimarães1000
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Comment: C: Convert VCFf file to plink ped/map format while filtering the SNPs
... I think you need samples in your vcf to calculate the minor allele frequency. If you are using --allow-no-samples your vcf might have no samples to calculate it from. ...
written 5 months ago by Raony Guimarães1000
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Answer: A: How to combine a multi sample VCF from multiple sample VCF?
... You could merge the files with bcftools: bcftools merge -O z -o merged.vcf.gz sample1.vcf.gz sample2.vcf.gz ...
written 7 months ago by Raony Guimarães1000
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Answer: A: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 201
... A map of constrained coding regions in the human genome https://www.nature.com/articles/s41588-018-0294-6 ...
written 7 months ago by Raony Guimarães1000
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Forum: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2018?
... What do you think were the most influential Bioinformatics/Computational Biology Papers/methods/discovery Of 2018? Previous Discussions [What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2017?][1] [What Are The Most Influential Bioinformatics/Computational Biology Paper ...
bioinformatics forum papers survey snp written 7 months ago by Raony Guimarães1000 • updated 7 months ago by zx87548.0k
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Answer: A: Redundant Group Of Proteins.
... I would try to find the minimum amount of common proteins between the 24 organisms. ...
written 8 months ago by Raony Guimarães1000
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Answer: A: How to convert vcf to MAF ?
... Perl method works well and is the most recommend :) https://github.com/mskcc/vcf2maf You don't necessarily need an EXaC vcf to annotate, but you will need VEP. ...
written 8 months ago by Raony Guimarães1000
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Answer: A: Comparing VCF files between two groups (15 vcf files against 15 vcf files)
... It really depends on what you want to achieve with this comparison. You could merge all VCFs and do an association analysis between the two populations using plink to find differences between the two groups or you could do a PCA using all samples to see if the two populations have a clear separation ...
written 8 months ago by Raony Guimarães1000

Latest awards to Raony Guimarães

Voter 5 months ago, voted more than 100 times.
Guru 7 months ago, received more than 100 upvotes.
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: How To Map The Fastq With Paired-End Seq Combined In One File
Scholar 8 months ago, created an answer that has been accepted. For A: genome browser with genomic coordinate
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How To Map The Fastq With Paired-End Seq Combined In One File
Scholar 17 months ago, created an answer that has been accepted. For A: genome browser with genomic coordinate
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How To Map The Fastq With Paired-End Seq Combined In One File
Popular Question 20 months ago, created a question with more than 1,000 views. For 1000 Genomes Yri Trio, Ncbi36/37 And Rs334
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: How To Map The Fastq With Paired-End Seq Combined In One File
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Great Question 2.2 years ago, created a question with more than 5,000 views. For Is It Nonsense To Have Sift/Polyphen2 Scores For Nonsense Variants ?
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Scholar 3.2 years ago, created an answer that has been accepted. For A: genome browser with genomic coordinate
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Popular Question 3.7 years ago, created a question with more than 1,000 views. For 1000 Genomes Yri Trio, Ncbi36/37 And Rs334
Scholar 4.1 years ago, created an answer that has been accepted. For A: genome browser with genomic coordinate
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