Moderator: Eric Normandeau

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Eric Normandeau9.9k
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Quebec, Canada
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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

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Comment: C: Where To Look For Quality Bioinformatics Short Courses And Workshops?
... The Assembly and Annotation of Genomes course was great. Thanks again for the knowledge we gained from your course. ...
written 3 months ago by Eric Normandeau9.9k
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Comment: C: Polishing PacBio assembly : The ideal coverage for higly polymorphic species
... Hi Roxanne. Thanks for the good info! What tool(s) did you use for polishing? Pilon? ...
written 5 months ago by Eric Normandeau9.9k
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Comment: C: Longer scaffolds from multiple eukaryote genome assemblies
... So basically treat contigs and scaffolds as long reads? That would mean VERY low coverage, on the order of 1 to 2. I'll explore this avenue but something tells me the assemblers are going to struggle with such a low coverage. ...
written 10 months ago by Eric Normandeau9.9k
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Comment: C: Longer scaffolds from multiple eukaryote genome assemblies
... Thanks. PBJelly has already been run on the PacBio assembly using the 10X reads but I never heard of OPERA-LG. I'll check it out. ...
written 10 months ago by Eric Normandeau9.9k
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Comment: C: Longer scaffolds from multiple eukaryote genome assemblies
... The Omicstools list is where I found GARM and Camsa. I sifted through the list and kept a few that looked promising. These two are my best bet for now. The fly is diploid. The genomes were not assembled from a double haploid individual. ...
written 10 months ago by Eric Normandeau9.9k
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Comment: C: Longer scaffolds from multiple eukaryote genome assemblies
... Yes, I am looking at GARM. See my edit above. ...
written 10 months ago by Eric Normandeau9.9k
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Comment: C: Longer scaffolds from multiple eukaryote genome assemblies
... Is FALCON supposed to be able to merge different assemblies produces by different technologies? ...
written 10 months ago by Eric Normandeau9.9k
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Longer scaffolds from multiple eukaryote genome assemblies
... I have two fly genomes from a species for which there are no other genomes available. One genome has been assembled from PacBio reads (N50=~400,000bp) and one from 10X (N50=~250,000bp). The genome is about 250-300Gb long. I would like to use the scaffolds from both these genomes to create an assemb ...
genome scaffolding written 10 months ago by Eric Normandeau9.9k • updated 7 months ago by harishk020120
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Comment: C: GAWN - Genome Annotation Without Nightmares
... You can put multiple transcriptomes in a single fasta file and pass it to GAWN. Just be aware that in the annotation you risk having multiple annotations at the same (or similar) positions on the genome. You could also add ESTs, RNA-seq assembled transcripts, etc, but you should avoid passing it a ...
written 10 months ago by Eric Normandeau9.9k
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Comment: C: Should PCR duplicates always be removed?
... Hi Fabio. Thanks for refering to my Github repository. However, my code is not the source of the STACKS package, just a set of scripts to manage GBS projects and run STACKS itself. STACKS can be found here: http://catchenlab.life.illinois.edu/stacks/ ...
written 10 months ago by Eric Normandeau9.9k

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