Moderator: Eric Normandeau

gravatar for Eric Normandeau
Eric Normandeau9.5k
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Quebec, Canada
Website:
http://github.com/enor...
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  • Biologist turned bioinformatician, fluent in Python, R, and bash, now learning Rust for fun

  • I have worked with microarrays, qRT-PCR and am currently mainly working with RADseq / GBS, and eDNA.

  • If you are new to Biostars, you can read the following: How to ask Good Questions on Technical and Scientific Forums

Posts by Eric Normandeau

<prev • 657 results • page 1 of 66 • next >
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Comment: C: Combining The Paired Reads From Illumina Run
... As I replied to you on GitHub: If you launch the command with " " at the end, it will tell the script to use a space as a separator. Your name format is a bit strange so possibly you'll need to test some other options. Please report if this solves your problem. If not, please contact me by email wit ...
written 7 days ago by Eric Normandeau9.5k
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Comment: C: Reliable Fastq compression programs
... I never felt 100% sure about any of the alternative compression softwares, so I continued depending on gzip at the cost of having to buy more disk space. I would still love to find a better way but a major tradeoff is that fasta.gz and fastq.gz can be read by most bioinfo pieces of software so devia ...
written 5 weeks ago by Eric Normandeau9.5k
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Comment: C: GAWN - Genome Annotation Without Nightmares
... Hi YNFan. 1. Ideally, you use a transcriptome from the species for which you want to annotate the genome. Alternatively, use a species that is close phylogenetically. 2. Here is a link to install the blast utilities and get the databases. https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs ...
written 6 weeks ago by Eric Normandeau9.5k
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Comment: C: Eukaryotic Genome Annotation in 2016
... I ended up developing a simpler genome annotation pipeline based on suggestions from a colleague. You can find more about it in this Biostar post: **GAWN - Genome Annotation Without Nightmares** https://www.biostars.org/p/265158/ ...
written 7 weeks ago by Eric Normandeau9.5k
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Answer: A: Simplest genome protein annotation pipeline possible
... I ended up developing a genome annotation pipeline based on suggestions from a colleague. You can find more about it in this Biostar post: **GAWN - Genome Annotation Without Nightmares** https://www.biostars.org/p/265158/ ...
written 7 weeks ago by Eric Normandeau9.5k
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Tool: GAWN - Genome Annotation Without Nightmares
... I'm working on **GAWN** [https://github.com/enormandeau/gawn][1], a genome annotation pipeline that produces fast results based on evidence from an available transcriptome. Popular genome annotation pipelines are usually difficult to install and use and take forever to run. That is, when they do no ...
genome annotation tool software written 7 weeks ago by Eric Normandeau9.5k • updated 6 weeks ago by YNFan0
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Comment: C: Simplest genome protein annotation pipeline possible
... JAMg looks a bit more complex than our current pipeline (which fails) and depends on some of the same software that fails on our genomes... ¯\\_(ツ)_/¯ ...
written 8 weeks ago by Eric Normandeau9.5k
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Comment: C: Simplest genome protein annotation pipeline possible
... Yes, I know firsthand that genome annotation and simple don't go hand in hand ;) I'm investigating JAMg. Thanks for the suggestion! ...
written 8 weeks ago by Eric Normandeau9.5k
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Comment: C: Simplest genome protein annotation pipeline possible
... In the end, it looks like Maker is still the best/correct approach... Eukaryote Genome Annotation needs some serious streamlining. ...
written 8 weeks ago by Eric Normandeau9.5k
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Simplest genome protein annotation pipeline possible
... I'm often playing with draft genomes of non-model species (mostly in fishes) and we need to annotate these genomes. In cases like this, we do not really care about putative proteins that are based on ORFs or any ab-initio methods. **What we really need is to get a GFF3 annotation file listing known ...
genome annotation proteins written 10 weeks ago by Eric Normandeau9.5k

Latest awards to Eric Normandeau

Appreciated 6 weeks ago, created a post with more than 5 votes. For C: What'S The Best Generic Scripting Tool For Bioinformatics?
Great Question 7 weeks ago, created a question with more than 5,000 views. For Correct Way To Parse A Fasta File In Python
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Appreciated 3 months ago, created a post with more than 5 votes. For C: What'S The Best Generic Scripting Tool For Bioinformatics?
Appreciated 5 months ago, created a post with more than 5 votes. For C: What'S The Best Generic Scripting Tool For Bioinformatics?
Great Question 5 months ago, created a question with more than 5,000 views. For Snp Detection And Genotyping In Ngs (Next Generation Sequencing)
Popular Question 5 months ago, created a question with more than 1,000 views. For Automate High-Volume Sequence Annotation And Genbank Submission
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Great Question 6 months ago, created a question with more than 5,000 views. For Snp Detection And Genotyping In Ngs (Next Generation Sequencing)
Epic Question 6 months ago, created a question with more than 10,000 views. For Correct Way To Parse A Fasta File In Python
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