Moderator: Leonor Palmeira

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Leonor Palmeira3.6k
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Liège, Belgium
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Scientist | Senior Bioinformatician @ CHU Liege, Belgium

 

Posts by Leonor Palmeira

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Job: Scientist in Bioinformatics for a genomic medicine project, GIGA Research Center, University of Liege, Liege, Belgium
... The GIGA Research Center (http://www.giga.ulg.ac.be) is a multidisciplinary research group at the University of Liège aiming at developing applied genomics and proteomics research programs. The CHU Liège is a University Hospital active in all the aspects of health care, including human genetics, onc ...
bioinformatics ngs medicine job diagnostics written 4 months ago by Leonor Palmeira3.6k • updated 4 months ago by genomax52k
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Job: Post-doctoral researcher for a genomic medicine project, University of Liege, Liege, Belgium
... The GIGA (http://www.giga.ulg.ac.be) is seeking for a post-doctoral researcher for a genomic medicine project. The GIGA Research Center is a multidisciplinary research group at the University of Liège aiming at developing applied genomics and proteomics research programs. The CHU Liège ...
bioinformatics next-gen medicine job diagnostics written 7 months ago by Leonor Palmeira3.6k • updated 7 months ago by genomax52k
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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 14 months ago by Leonor Palmeira3.6k
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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 3.1 years ago by Leonor Palmeira3.6k
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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 3.7 years ago by Leonor Palmeira3.6k
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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 3.7 years ago by Leonor Palmeira3.6k
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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 3.7 years ago by Leonor Palmeira3.6k
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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 3.7 years ago by Leonor Palmeira3.6k
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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 3.7 years ago by Leonor Palmeira3.6k
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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 3.7 years ago by Leonor Palmeira3.6k

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Appreciated 14 months ago, created a post with more than 5 votes. For A: Woman Sequenced With 454 Technology?
Popular Question 14 months ago, created a question with more than 1,000 views. For Amino Acid Change To Genomic Location: using 'backlocate'
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Which Journals Should I Follow If I Write Software And Algorithms In Computation
Appreciated 14 months ago, created a post with more than 5 votes. For A: K-Mer Analysis
Popular Question 17 months ago, created a question with more than 1,000 views. For Amino Acid Change To Genomic Location: using 'backlocate'
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Is there a tool to transform GenomeStudio genotype format to VCF?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Find Papers That Use A Given Pdb Structure
Commentator 3.1 years ago, created a comment with at least 3 up-votes. For C: Thoughts On Galaxy For Next Generation Sequence Data Analysis
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Ngs Course Medical Genomics, Leuven, 17-20 September 2013
Popular Question 3.2 years ago, created a question with more than 1,000 views. For How To Force 'Bwa Samse' To Output Multiple Hits In .Sam Format?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Find Papers That Use A Given Pdb Structure
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: Woman Sequenced With 454 Technology?
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Find Papers That Use A Given Pdb Structure
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