User: Roxane Boyer

gravatar for Roxane Boyer
Roxane Boyer870
Reputation:
870
Status:
Trusted
Location:
France / Toulouse / GeT-Plage
Last seen:
7 hours ago
Joined:
2 years, 6 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 • 204 results • page 1 of 21 • next >
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Answer: A: PacBio sequencing for variant calling?
... Hello Borealis ! I think this paper may help you : https://www.nature.com/articles/s41592-018-0001-7 (the free bioarxiv here ;) : https://www.biorxiv.org/content/biorxiv/early/2017/07/28/169557.full.pdf ) It explains how long read sequencing (such as ONT and PacBio methods) can help finding large ...
written 4 days ago by Roxane Boyer870 • updated 4 days ago by genomax60k
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Comment: C: First time using maker
... Very nice to know ! So how did it went in the end ? Was the annotation good with the spliting process ? ...
written 10 days ago by Roxane Boyer870
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Comment: C: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... Hello again Cecilio ! To make it clear here, the reference I"m talking about here ... > aligning your raw PacBio reads against the reference (your freshly > baked PacBio assembly) ...is actually your assembly. So it means you have to align your raw reads against the assembly you just made. ...
written 5 weeks ago by Roxane Boyer870
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Comment: C: First time using maker
... Hello Imda ! 1) If you don't have any RNAseq data from the species you want to annotate, you can still use proteins evidences from several closely related species. But I won't advice to do so, I think the best way to annotate a genome is using EST from the same species if you want it to be accurate ...
written 5 weeks ago by Roxane Boyer870
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Comment: C: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... Hi Cecilio ! You're welcome, glad this could help ! Concerning your issue, so you are doing *do novo* genome assembly. Do you have the estimated size of the bacteria's genome ? What sequencing technology did you used ? (pacbio ? illumina ?) In my opinion, you don't necessarily need a genome refere ...
written 7 weeks ago by Roxane Boyer870
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Comment: C: Remove adaptaters from ONT reads : An alternative to Porechop ?
... The hype is real o_o ...
written 9 weeks ago by Roxane Boyer870
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Comment: C: Remove adaptaters from ONT reads : An alternative to Porechop ?
... I see ;) Bacterial genome with 15000X for the win o/ ...
written 9 weeks ago by Roxane Boyer870
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Comment: C: Remove adaptaters from ONT reads : An alternative to Porechop ?
... "Near future" ;) Alright, I see, Thanks for the insight then. I'll keep play with Deepbiner tho, because it claims the result contain less than the 30% unclassified reads... Did you ever tried that tool ? ...
written 9 weeks ago by Roxane Boyer870
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Remove adaptaters from ONT reads : An alternative to Porechop ?
... Hello everyone, I was using Porechop (as everyone I guess) in order to remove adaptaters from ONT reads. This tools is now unsuported (https://www.biostars.org/p/282767/#282775 , https://github.com/rrwick/Porechop), and with rapid changes in ONT softwares, I'm really afraid it will soon be impossib ...
promethion minion ont gridion oxford nanopore written 9 weeks ago by Roxane Boyer870 • updated 9 weeks ago by WouterDeCoster35k
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Comment: C: Nanopore only assembly errors
... Hello karthick ! Which tools did you used to asses % of indels before and after polishing ? And also how much coverage did you used for polishing with Nanopolish ? Just for my own curiosity ! Cheers, Roxane ...
written 12 weeks ago by Roxane Boyer870

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Popular Question 1 day ago, created a question with more than 1,000 views. For Canu assembler : meryl failed after 2 attempts
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Teacher 2 days ago, created an answer with at least 3 up-votes. For A: What can I do after my Pacbio genome assembly ?
Popular Question 29 days ago, created a question with more than 1,000 views. For Canu assembler : meryl failed after 2 attempts
Popular Question 29 days 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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Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: What can I do after my Pacbio genome assembly ?
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Popular Question 11 months ago, created a question with more than 1,000 views. For First time using maker
Popular Question 11 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 13 months ago, created a question with more than 1,000 views. For Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone

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