User: Roxane Boyer

gravatar for Roxane Boyer
Roxane Boyer700
Reputation:
700
Status:
Trusted
Location:
France / Toulouse / GeT-Plage
Last seen:
2 days, 5 hours ago
Joined:
2 years, 2 months ago
Email:
r*************@gmail.com

Recently started to work on the Toulouse sequencing platforme GeT-Plage, attached to the French National Institute of Agronomic Research (INRA). I'll most be dealing with Oxford Nanopore generated data.

Posts by Roxane Boyer

<prev • 193 results • page 1 of 20 • next >
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Comment: C: Looking for a file : Complete Ref Seq Systematic Classification
... Thanks a lot that was exactly what I was looking for ! Have a nice day :) ...
written 19 days ago by Roxane Boyer700
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Looking for a file : Complete Ref Seq Systematic Classification
... Hello Biostar, I'm sorry if this is an innapropriate place to ask for it, but I can't find this file by myself and actually don't know if it exist. I'm looking for a file containing the whole systematic classification of RefSeq, I have a table that would look like this in mind : https://www.encyc ...
classification written 20 days ago by Roxane Boyer700 • updated 20 days ago by Sej Modha3.6k
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Comment: C: Using the right reference to identify sequences origin
... I have therefore an other question : don't you think that this tool, which kinda compress a sequence using it's most representative k-mers, would be a lot impacted by the used sequencing technolgy ? Both for the raw reads than for the resulting assemblies. Raw PacBio/ONT reads are longer but more er ...
written 4 weeks ago by Roxane Boyer700
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Comment: C: Using the right reference to identify sequences origin
... I can understand why ! I still need to try out few more test in order to make it fit my purpose tho. Because for now a mash dist with whole refseq and a fastq of fish sequence best matche with mammals genome before fish genomes... If you have any kind of experience with parameters I should use to bu ...
written 4 weeks ago by Roxane Boyer700
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Comment: C: Using the right reference to identify sequences origin
... This tool is awesome... Making a lot of test with it and it's a fast and smart approache... Thanks a lot for advising that to me ! ...
written 4 weeks ago by Roxane Boyer700
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Comment: C: Using the right reference to identify sequences origin
... Does the idea of constructing a hybrid fasta file containing several genome of a specified target I want to identify seems to be shocking according to you ? I realise it may be the main point of my post in the end. ...
written 4 weeks ago by Roxane Boyer700
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Comment: C: Using the right reference to identify sequences origin
... Thanks, I'll have a look on it, but as I said to genomax, I'm not really asking for advices on a tool, but rather on how should I build my own small reference database... ;( ...
written 4 weeks ago by Roxane Boyer700
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Comment: C: Using the right reference to identify sequences origin
... What scare me with Diamond is that is seems to be too heavy for the simple purpose I want to accomplish. And it is not even suited for ONT Long reads. I'm not at the stage anymore where I'm looking for tools (unless what I want exist but I didn't saw it). I think I'm going to use a "homemade" soluti ...
written 4 weeks ago by Roxane Boyer700
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Comment: C: Using the right reference to identify sequences origin
... The main reason I'm not selecting what I want is because the sequences I'm producing may be from de novo sequencing. But indeed I guess such an approache could work. Isn't BBSplit going to discard the reads I don't want tho ? Because this is not what I am aiming for. I would like just to report what ...
written 4 weeks ago by Roxane Boyer700
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Using the right reference to identify sequences origin
... Hello Biostar, I have a question I'm unable to answer myself for several weeks now. I would like to add a new QC analysis to my pipeline (ONT data) which would be able to both : - detect if our sequences contains any contaminants (bacteria ? virus ? human DNA ?) - detect if the sequences ...
genome sequence written 4 weeks ago by Roxane Boyer700 • updated 4 weeks ago by 5heikki7.6k

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For First time using maker
Prophet 9 weeks ago, created a post with more than 20 followers. For Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
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Scholar 10 weeks ago, created an answer that has been accepted. For A: Polishing PacBio assembly : The ideal coverage for higly polymorphic species
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Popular Question 4 months ago, created a question with more than 1,000 views. For First time using maker
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Popular Question 4 months ago, created a question with more than 1,000 views. For What are the ".bax.h5" files generated by PacBio long reads sequencing ?
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Popular Question 7 months ago, created a question with more than 1,000 views. For What are the ".bax.h5" files generated by PacBio long reads sequencing ?
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