User: alesssia

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alesssia560
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560
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London, UK
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_alesssia
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1 month, 3 weeks ago
Joined:
5 years, 4 months ago
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a***************@gmail.com

Postdoc in Computational Biology, master Googler, experienced programmer, genetics learner. 

The majority of my day consists of software development and population genetics analyses. I mostly torture data until they confess. 

 

 

Posts by alesssia

<prev • 112 results • page 1 of 12 • next >
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Genetic correlation with related individuals
... Dear all, I am aiming at evaluating the genetic correlation among ~150 continuous traits measured in ~1100 twin pairs (~2200 individuals). I have already run GWASs for each trait (using an LMM as implemented in GEMMA), therefore, I have both the genetic data and the GWAS summary statistics. I had ...
ldsc genetic correlation bolt-reml gcta gwas written 10 weeks ago by alesssia560
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Computational resources for WGS variant calling
... Dear all, we have WGS data for about 2000 individuals (30x, ~100G per file). We would like to align them using bwakit, and then perform the variant calling using GATK haplotype caller, something I have never done before at this scale (and with such large files) We have limited computational resour ...
variant calling wgs bwakit openstack gatk written 6 months ago by alesssia560 • updated 4 months ago by Jeremy Leipzig19k
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Chromosome X GWAS in related individuals
... Dear all, I would like to include the X Chromosome in a GWAS of a continuous trait which has been measured in a dataset of related individuals (same-sex twins, ~22% males, 78% females). I had a look at the literature, but most of the approaches presented seems to focus on case-control studies rath ...
gemma chromosome x related individuals gwas written 14 months ago by alesssia560 • updated 14 months ago by Kevin Blighe60k
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Can I run the EBI metagenomics pipeline locally?
... Hello everyone, I was wondering whether the EBI metagenomics pipeline ( https://www.ebi.ac.uk/metagenomics/ ) could be run locally. Here https://emg-docs.readthedocs.io/en/latest/_images/pipeline_v4.1b_overview.png there is an overview of the processing flow which specifies the software used and so ...
ebi metagenomics pipeline written 2.2 years ago by alesssia560 • updated 2.2 years ago by h.mon29k
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Comment: C: Metagenome Read Simulators
... Good point. Since I need to keep the percentage of duplicates equal to fixed values I should first check if there are any and add/remove if needed! Thanks! ...
written 2.2 years ago by alesssia560
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Comment: C: Metagenome Read Simulators
... Thanks, I think I will just generate the metagenomics samples, then randomly select varying percentage of reads, duplicate them, and finally shuffle their quality score. Will this work in your opinion? ...
written 2.2 years ago by alesssia560
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Metagenome Read Simulators
... Hello everyone, I need to simulate a few metagenomics samples and I was thinking to use BBMap's simulator, randomreads.sh, in "metagenome" mode. The problem is that I need to simulate the effect of PCR amplification, and I thought of including identical duplicates but with different quality score ...
wgs metagenomics bbmap simulation written 2.2 years ago by alesssia560
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Comment: C: Plot with locuszoom and chr:pos SNPs
... This specific question regarded the online version of LocusZoom ([http://locuszoom.org/genform.php?type=yourdata][1], "Genome Build/LD Population" field). If you use the standalone version, they should be downloaded along with the main app ([https://statgen.sph.umich.edu/locuszoom/download/][2]), an ...
written 3.1 years ago by alesssia560
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Comment: C: Plot with locuszoom and chr:pos SNPs
... This specific question regarded the online version of LocusZoom ([http://locuszoom.org/genform.php?type=yourdata][1], "Genome Build/LD Population" field). If you use the standalone version, they should be downloaded along with the main app ([https://statgen.sph.umich.edu/locuszoom/download/][2]), an ...
written 3.1 years ago by alesssia560
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Comment: C: Metagenomics data: trimming and decontamination
... I see, sorry! Thanks a lot! ...
written 3.3 years ago by alesssia560

Latest awards to alesssia

Student 4 months ago, asked a question with at least 3 up-votes. For Computational resources for WGS variant calling
Popular Question 13 months ago, created a question with more than 1,000 views. For Recommendation on tutorials/books for longitudinal data analysis
Student 2.0 years ago, asked a question with at least 3 up-votes. For How to remove batch effect from RNA-seq data?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Conditional analysis with duplicate variant IDs in PLINK
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Conditional analysis with duplicate variant IDs in PLINK
Great Question 2.8 years ago, created a question with more than 5,000 views. For How to remove batch effect from RNA-seq data?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Conditional analysis with duplicate variant IDs in PLINK
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Recommendation on tutorials/books for longitudinal data analysis
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Sanger Imputation Service - The input file sanity check failed
Popular Question 2.8 years ago, created a question with more than 1,000 views. For How to remove batch effect from RNA-seq data?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Sanger Imputation Service - The input file sanity check failed
Popular Question 3.0 years ago, created a question with more than 1,000 views. For How to remove batch effect from RNA-seq data?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Sanger Imputation Service - The input file sanity check failed
Centurion 3.3 years ago, created 100 posts.
Supporter 3.5 years ago, voted at least 25 times.
Popular Question 3.8 years ago, created a question with more than 1,000 views. For DESeq2: invalid class “GRangesList” object
Popular Question 3.8 years ago, created a question with more than 1,000 views. For PLINK: Unrecognized flag '--list-duplicate-vars'
Popular Question 3.8 years ago, created a question with more than 1,000 views. For lmekin -- Model fails because of the Cholesky decomposition -- but chol works!
Popular Question 4.2 years ago, created a question with more than 1,000 views. For How to remove batch effect from RNA-seq data?
Popular Question 4.3 years ago, created a question with more than 1,000 views. For How to remove batch effect from RNA-seq data?
Scholar 4.9 years ago, created an answer that has been accepted. For A: Program to find genes up/down-regulated by a given gene
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: R programming, concatenate or combine all the column contents
Good Answer 5.0 years ago, created an answer that was upvoted at least 5 times. For A: R programming, concatenate or combine all the column contents
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Scholar 5.0 years ago, created an answer that has been accepted. For A: Program to find genes up/down-regulated by a given gene

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