Moderator: Eric Normandeau

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Eric Normandeau9.6k
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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: 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 2 days ago by Eric Normandeau9.6k
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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 2 days ago by Eric Normandeau9.6k
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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 2 days ago by Eric Normandeau9.6k
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Comment: C: Longer scaffolds from multiple eukaryote genome assemblies
... Yes, I am looking at GARM. See my edit above. ...
written 2 days ago by Eric Normandeau9.6k
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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 2 days ago by Eric Normandeau9.6k
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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 2 days ago by Eric Normandeau9.6k • updated 2 days ago by Sergey Naumenko220
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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 6 days ago by Eric Normandeau9.6k
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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 6 days ago by Eric Normandeau9.6k
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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 10 weeks ago by Eric Normandeau9.6k
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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 3 months ago by Eric Normandeau9.6k

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