Moderator: Eric Normandeau

gravatar for Eric Normandeau
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Location:
Quebec, Canada
Website:
http://github.com/enor...
Last seen:
1 week ago
Joined:
8 years, 9 months ago
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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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Answer: A: scRNA-seq data analysis Workshop in Berlin
... I highly encourage people to look for Physalia courses on subjects that interest them. I have personally attended the Assembly of Genomes course in Berlin, which was excellent, and we are currently hosting two Physalia courses in Canada (a first!) on Population Genomics and eDNA Metabarcoding. ...
written 9 weeks ago by Eric Normandeau10k
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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 7 months ago by Eric Normandeau10k
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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 9 months ago by Eric Normandeau10k
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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 14 months ago by Eric Normandeau10k
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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 14 months ago by Eric Normandeau10k
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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 14 months ago by Eric Normandeau10k
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Comment: C: Longer scaffolds from multiple eukaryote genome assemblies
... Yes, I am looking at GARM. See my edit above. ...
written 14 months ago by Eric Normandeau10k
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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 14 months ago by Eric Normandeau10k
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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 14 months ago by Eric Normandeau10k • updated 11 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 14 months ago by Eric Normandeau10k

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Popular Question 9 months ago, created a question with more than 1,000 views. For Where is it possible to submit annotated eukaryote genomes?
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