User: Raony Guimarães
Raony Guimarães • 820
- Reputation:
- 820
- Status:
- Trusted
- Location:
- Dublin / Ireland
- Website:
- https://raonyguimaraes...
- Twitter:
- raonyguimaraes
- Scholar ID:
- Google Scholar Page
- Last seen:
- 12 hours ago
- Joined:
- 6 years, 10 months ago
- Email:
- r*************@gmail.com
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
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2
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194
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Answer:
A: Clustering large data
... You could use scikit-learn http://scikit-learn.org
http://scikit-learn.org/stable/modules/clustering.html#clustering ...
written 3 months ago by
Raony Guimarães • 820
3
votes
5
answers
406
views
5
answers
... Hi there,
Just want to say I made [mendelmd.org][1] for that.
It's free and open source!
[1]: http://mendelmd.org ...
written 4 months ago by
Raony Guimarães • 820
0
votes
1
answer
313
views
1
answers
Answer:
A: VQSRTranche filters in GATK
... This image explains more about the tranches
 ...
written 5 months ago by
Raony Guimarães • 820
0
votes
3
answers
534
views
3
answers
... You need to provide a bed file with the target regions specific to your exome target kit or you can use a generic with the official list of exome regions from UCSC.
...
written 5 months ago by
Raony Guimarães • 820
0
votes
1
answer
631
views
1
answers
Comment:
C: GATK Unified Genotyper
... Yes, this is only a warning. ...
written 5 months ago by
Raony Guimarães • 820
0
votes
1
answer
631
views
1
answers
Answer:
A: GATK Unified Genotyper
... This is likely happening because you are not giving enough memory to java with the parameter: -Xmx
Try running it again with the following command:
java -Xmx 32g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -R hg38.fa -I /home/likithreddy/Documents/Cancergenomics/ReadgroupsSRR098401mem_pesort.ba ...
written 5 months ago by
Raony Guimarães • 820
2
votes
2
answers
1.4k
views
2
answers
Answer:
A: Number of Threads for BWA MEM
... Are you looking for something like this ?
Source: http://en.community.dell.com/techcenter/high-performance-computing/b/genomics ...
written 5 months ago by
Raony Guimarães • 820
0
votes
2
answers
271
views
2
answers
... Are you looking for Blast2GO ?
"Blast2GO offers the possibility of direct statistical analysis on gene function information. A common analysis is the statistical assessment of GO term enrichment in a group of interesting genes when compared to a reference group i.e. to asses the functional differen ...
written 5 months ago by
Raony Guimarães • 820
0
votes
2
answers
312
views
2
answers
Answer:
A: SNP single end read
... Yes it's possible.
Take a look at:
DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.
https://github.com/GATB/DiscoSnp
Reference-free SNP detection: dealing with the data deluge
https://www.ncbi.nlm.nih. ...
written 5 months ago by
Raony Guimarães • 820
0
votes
2
answers
1.1k
views
2
answers
... That depends on multiple factors such as sample origin, exome kit, parameters used for alignment and variant calling. Usually after filtering and annotating the final VCF with Snpeff or VEP and restricting your variant list only to the exon regions you should get between 20-40k variants. ...
written 5 months ago by
Raony Guimarães • 820
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For A: genome browser with genomic coordinate
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For A: How To Map The Fastq With Paired-End Seq Combined In One File
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For 1000 Genomes Yri Trio, Ncbi36/37 And Rs334
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For A: How To Map The Fastq With Paired-End Seq Combined In One File
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11 months ago,
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For A: How To Map The Fastq With Paired-End Seq Combined In One File
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For Is It Nonsense To Have Sift/Polyphen2 Scores For Nonsense Variants ?
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16 months ago,
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For A: How To Map The Fastq With Paired-End Seq Combined In One File
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24 months ago,
created an answer that has been accepted.
For A: genome browser with genomic coordinate
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2.3 years 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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created a question with more than 1,000 views.
For 1000 Genomes Yri Trio, Ncbi36/37 And Rs334
Scholar
3.0 years ago,
created an answer that has been accepted.
For A: genome browser with genomic coordinate
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For Is It Nonsense To Have Sift/Polyphen2 Scores For Nonsense Variants ?
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For Is It Nonsense To Have Sift/Polyphen2 Scores For Nonsense Variants ?
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For A: How Important Is It To Gather New Controls For Whole Genome And Exome Variant St
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5.4 years ago,
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For A: How To Map The Fastq With Paired-End Seq Combined In One File
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For A: Machine Learning Tutorials In Python
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For A: Machine Learning Tutorials In Python
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For Chip-Seq Data Analysis
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For A: Gatk Alignertargetcreator Error
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