Moderator: Leonor Palmeira

gravatar for Leonor Palmeira
Leonor Palmeira3.5k
Reputation:
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Location:
Liège, Belgium
Website:
http://sites.google.co...
Last seen:
4 months, 1 week ago
Joined:
6 years, 6 months ago
Email:
l********@chu.ulg.ac.be

I am mainly interested in studying evolution through the use of computational biology approaches. I have been working on sequence analysis, comparative genomics and related topics such as evolutionary models for phylogeny, protein family clustering, conserved domains recognition. I am now more specifically focused on the evolution of viruses, and in particular of herpesviruses.

Posts by Leonor Palmeira

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Comment: C: BamUtil for Base Qual Recalibration
... This question is now 2.5 years old... With some hope : has anyone some information on performances of bamUtil compared to BQSR (not time performances but benchmarking or such) ? I would greatly appreciate any pointers! ...
written 4 months ago by Leonor Palmeira3.5k
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Job: Bioinformatician | NGS Diagnostic Testing @ Dept. Hum. Gen., Liege Univ. Hospital, BELGIUM
... The department of Human Genetics of the University Hospital of Liège is looking for a bioinformatician who is interested in designing, developing, and managing data analysis solutions that have direct impact on Medical management of patients. Our department develops NGS diagnostics tests in the fi ...
data science bioinformatics ngs job diagnostics written 2.2 years ago by Leonor Palmeira3.5k
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Comment: C: Retrieve Subset Positions Vcf File
... @Rm: You are right. Now that's a strange move... The latest 1.1 version I have just downloaded (tabix is now part of HTSlib) doesn't allow for the -B option although the manual (again out-of-date) still indicates it does: http://www.htslib.org/doc/tabix-1.1.html ...
written 2.9 years ago by Leonor Palmeira3.5k
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Comment: C: Retrieve Subset Positions Vcf File
... @Rm: can you tell us where you have seen this? The online manual is outdated and from version 0.1.1. I have version 0.2.5 (r964) with the option. It wouldn't make much sense to me to remove that option...   ...
written 2.9 years ago by Leonor Palmeira3.5k
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Comment: C: Use Tabix With A List Of Regions
... @Greg P: I think Rm is talking about the outdated manual available here, I haven't seen that the -B option has been dropped (wouldn't make much sense to me either). ...
written 2.9 years ago by Leonor Palmeira3.5k
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Answer: A: Use Tabix With A List Of Regions
... Tabix has a -B option which allows you to input a .bed file of regions of interest: tabix -fhB ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr12.phase1.projectConsensus.genotypes.vcf.gz regions.bed > genotypes.vcf   ...
written 2.9 years ago by Leonor Palmeira3.5k
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Comment: C: Author affiliation and for-profit licensing of published software
... It's basically the same thing in France concerning intellectual property rights: they are owned by the employing institution. Although I'm not sure we actually sign anything when beginning employment.   ...
written 2.9 years ago by Leonor Palmeira3.5k
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Answer: A: What Are The Open Source Alternatives To Gatk?
... There is a recent duplicate of this question that has very interesting information: https://www.biostars.org/p/114770 ...
written 2.9 years ago by Leonor Palmeira3.5k
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Comment: C: Gatk - Haplotypecaller Is So Slow, What Is Faster And As Good?
... The Platypus paper is out: http://www.nature.com/ng/journal/v46/n8/full/ng.3036.html ...
written 2.9 years ago by Leonor Palmeira3.5k
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Amino Acid Change To Genomic Location: using 'backlocate'
... I am moving the comment I made here (whatever not displayed) to a real question: I am trying to use backlocate to get the genomic position (say, on hg19) from a mutation given with the classic nomenclature: p.D240Y (gene EIF4G1). There are two versions of the tool available: - one from github - ...
backlocate mutation hg19 written 2.9 years ago by Leonor Palmeira3.5k • updated 2.9 years ago by Pierre Lindenbaum98k

Latest awards to Leonor Palmeira

Popular Question 7 months ago, created a question with more than 1,000 views. For Amino Acid Change To Genomic Location: using 'backlocate'
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Is there a tool to transform GenomeStudio genotype format to VCF?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Find Papers That Use A Given Pdb Structure
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Thoughts On Galaxy For Next Generation Sequence Data Analysis
Popular Question 2.4 years ago, created a question with more than 1,000 views. For How To Force 'Bwa Samse' To Output Multiple Hits In .Sam Format?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Ngs Course Medical Genomics, Leuven, 17-20 September 2013
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Find Papers That Use A Given Pdb Structure
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Woman Sequenced With 454 Technology?
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Find Papers That Use A Given Pdb Structure
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Find Papers That Use A Given Pdb Structure
Scholar 3.3 years ago, created an answer that has been accepted. For A: How To Force 'Bwa Samse' To Output Multiple Hits In .Sam Format?
Guru 3.4 years ago, received more than 100 upvotes.
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Appreciated 4.1 years ago, created a post with more than 5 votes. For C: Converting Gene Predictions In Glimmer To Protein Sequences.
Commentator 4.1 years ago, created a comment with at least 3 up-votes. For C: Converting Gene Predictions In Glimmer To Protein Sequences.
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: How To Plot A Circular Genome Map?
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: Find Papers That Use A Given Pdb Structure
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: How Can One Cpg Locus Have Both Methylated And Unmethylated Signals? (Illumina 4
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Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Can A Bioinformatician Go Back To Biology In A Phd

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