User: alesssia

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alesssia530
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530
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Location:
London, UK
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_alesssia
Last seen:
6 months, 1 week ago
Joined:
4 years, 9 months ago
Email:
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 • 110 results • page 1 of 11 • next >
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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 7 months ago by alesssia530 • updated 7 months ago by Kevin Blighe51k
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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 19 months ago by alesssia530 • updated 19 months ago by h.mon28k
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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 19 months ago by alesssia530
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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 19 months ago by alesssia530
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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 20 months ago by alesssia530
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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 2.6 years ago by alesssia530
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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 2.6 years ago by alesssia530
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Comment: C: Metagenomics data: trimming and decontamination
... I see, sorry! Thanks a lot! ...
written 2.7 years ago by alesssia530
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Comment: C: Metagenomics data: trimming and decontamination
... Do you mean here? https://github.com/BioInfoTools/BBMap (https://github.com/BioInfoTools/BBMap/tree/master/resources) ...
written 2.7 years ago by alesssia530
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Comment: C: Metagenomics data: trimming and decontamination
... BBmap has been installed by our IT team, and the resources directory seems to be empty (I've downloaded phix174_ill.ref.fa.gz and adapters.fa from the GitHub, but I haven't found sequencing_artifacts.fa.gz there). Will investigate with them :) I've quickly read about bbsplit, but it is not clear to ...
written 2.7 years ago by alesssia530

Latest awards to alesssia

Student 17 months ago, asked a question with at least 3 up-votes. For How to remove batch effect from RNA-seq data?
Popular Question 19 months ago, created a question with more than 1,000 views. For Conditional analysis with duplicate variant IDs in PLINK
Popular Question 19 months ago, created a question with more than 1,000 views. For Conditional analysis with duplicate variant IDs in PLINK
Great Question 2.2 years ago, created a question with more than 5,000 views. For How to remove batch effect from RNA-seq data?
Popular Question 2.2 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 Recommendation on tutorials/books for longitudinal data analysis
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Sanger Imputation Service - The input file sanity check failed
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to remove batch effect from RNA-seq data?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Sanger Imputation Service - The input file sanity check failed
Popular Question 2.5 years ago, created a question with more than 1,000 views. For How to remove batch effect from RNA-seq data?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Sanger Imputation Service - The input file sanity check failed
Centurion 2.7 years ago, created 100 posts.
Supporter 3.0 years ago, voted at least 25 times.
Popular Question 3.2 years ago, created a question with more than 1,000 views. For DESeq2: invalid class “GRangesList” object
Popular Question 3.2 years ago, created a question with more than 1,000 views. For PLINK: Unrecognized flag '--list-duplicate-vars'
Popular Question 3.2 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 3.7 years ago, created a question with more than 1,000 views. For How to remove batch effect from RNA-seq data?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For How to remove batch effect from RNA-seq data?
Scholar 4.4 years ago, created an answer that has been accepted. For A: Program to find genes up/down-regulated by a given gene
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: R programming, concatenate or combine all the column contents
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: R programming, concatenate or combine all the column contents
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: R programming, concatenate or combine all the column contents
Scholar 4.5 years ago, created an answer that has been accepted. For A: Program to find genes up/down-regulated by a given gene
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: R programming, concatenate or combine all the column contents
Scholar 4.5 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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