User: alesssia

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alesssia510
Reputation:
510
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Location:
London, UK
Twitter:
_alesssia
Last seen:
9 months, 4 weeks ago
Joined:
4 years, 1 month 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 • 109 results • page 1 of 11 • next >
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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 11 months ago by alesssia510 • updated 11 months ago by h.mon24k
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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 12 months ago by alesssia510
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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 12 months ago by alesssia510
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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 12 months ago by alesssia510
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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 23 months ago by alesssia510
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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 23 months ago by alesssia510
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Comment: C: Metagenomics data: trimming and decontamination
... I see, sorry! Thanks a lot! ...
written 2.1 years ago by alesssia510
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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 2.1 years ago by alesssia510
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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 2.1 years ago by alesssia510
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Comment: C: Metagenomics data: trimming and decontamination
... Hi Brian, after much more talking, we decided to move from Trim Galore! to BBduk and from deconseq to BBmap (60% faster, that's amazing!), as you suggested on your first answer! I have, however, a few more questions :$ My trimming command is as following: > bbduk.sh -Xmx16g in=mysample_dedupe ...
written 2.1 years ago by alesssia510

Latest awards to alesssia

Popular Question 11 months ago, created a question with more than 1,000 views. For Conditional analysis with duplicate variant IDs in PLINK
Popular Question 11 months ago, created a question with more than 1,000 views. For Conditional analysis with duplicate variant IDs in PLINK
Great Question 19 months ago, created a question with more than 5,000 views. 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 Recommendation on tutorials/books for longitudinal data analysis
Popular Question 19 months ago, created a question with more than 1,000 views. For Sanger Imputation Service - The input file sanity check failed
Popular Question 19 months ago, created a question with more than 1,000 views. For How to remove batch effect from RNA-seq data?
Popular Question 22 months ago, created a question with more than 1,000 views. For Sanger Imputation Service - The input file sanity check failed
Popular Question 22 months ago, created a question with more than 1,000 views. For How to remove batch effect from RNA-seq data?
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Popular Question 2.5 years ago, created a question with more than 1,000 views. For DESeq2: invalid class “GRangesList” object
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Popular Question 2.5 years ago, created a question with more than 1,000 views. For lmekin -- Model fails because of the Cholesky decomposition -- but chol works!
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