User: Alexandre Drouin

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60
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Trusted
Location:
Montreal, Canada
Website:
http://graal.ift.ulava...
Twitter:
alexandredrouin
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Google Scholar Page
Last seen:
2 days, 22 hours ago
Joined:
3 years, 8 months ago
Email:
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PhD Candidate @ Université Laval

Machine learning + Computational biology

Posts by Alexandre Drouin

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Create Dataset from reads -- IndexError: list index out of range
... @yusuf.sgs, did this resolve your issue? You can also reach out by email if you need further assistance. Cheers, Alex ...
written 29 days ago by Alexandre Drouin60
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Comment: C: Create Dataset from reads -- IndexError: list index out of range
... Hi Yusuf, sorry for the delayed response. It looks like the dataset file was not created correctly or is corrupted. I've seen this happen before when the DSK (the tool used for k-mer counting) was not compiled properly during the installation process. 1. Can you show me the output of `h5ls test` ...
written 6 weeks ago by Alexandre Drouin60
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Answer: A: Create Dataset from reads -- IndexError: list index out of range
... Hi there! The "where_read.tsv" file should have the format `GENOMEID{TAB}DIRECTORY_CONTAINING_READ_FILES`. The first column is a unique identifier for each genome (not the name of the read file). The second column is the path to a directory that contains all read files for that specific genome. Sim ...
written 8 weeks ago by Alexandre Drouin60
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Answer: A: Running kover do not work
... There are two main modules to kover: 1. Kover Dataset: takes care of packaging sequence data and phenotypes into a format on which machine learning analysis can be done efficiently (see: http://aldro61.github.io/kover/doc_dataset.html) 2. Kover learn: takes care of the machine learning analysis, ...
written 3 months ago by Alexandre Drouin60
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Answer: A: kover : UnboundLocalError: local variable 'genome_ids' referenced before assignm
... Hi Rania, We resolved this via email, but I'm posting some info here in case someone else encounters the same issue. Here are a few comments about the command line that was used: - --output should be the path to the kover dataset that will be generated. I would recommend calling this ../.. ...
written 3 months ago by Alexandre Drouin60 • updated 3 months ago by h.mon29k
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Answer: A: error while creating kover dataset from fastq
... Sorry for the late reply. It's the first time that I see this exception come out of DSK (the k-mer counter used by kover). Could you please show me a few lines of genomes.tsv and metadata.tsv? If you're able to share one of your fastq.gz files it would also be very useful. Thanks! Alex ...
written 16 months ago by Alexandre Drouin60
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Answer: A: Additional data for different isolates and antibiotics
... Hi! Yes, you can definitely get more data to train kover. The best source for antibiotic resistance datasets is the PATRIC database: https://www.patricbrc.org. I created a Python package to extract data from it: https://github.com/aldro61/patric_tools. Particularly, have a look at this script that ...
written 22 months ago by Alexandre Drouin60
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Comment: C: Kover - order of metadata
... It would definitely help me look into this if you were able to share your data. Would you be able to upload it to a server (e.g.: https://mega.nz/) and share the link? Also, can you include the kover commands that you are using to create and split the data? Did you set the random seed parameter in ...
written 3.1 years ago by Alexandre Drouin60
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Comment: C: kover installation problem: include could not find load file: GatbCore
... You're right. Sorry about that! ...
written 3.1 years ago by Alexandre Drouin60
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Comment: C: kover installation problem: include could not find load file: GatbCore
... Could you please add the "kover" tag to your post? ...
written 3.1 years ago by Alexandre Drouin60

Latest awards to Alexandre Drouin

Popular Question 22 months ago, created a question with more than 1,000 views. For Kover will provide support via Biostars
Scholar 3.1 years ago, created an answer that has been accepted. For A: kover installation problem: include could not find load file: GatbCore
Autobiographer 3.7 years ago, has more than 80 characters in the information field of the user's profile.

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