User: Roxane Boyer
Roxane Boyer • 870
- 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 >
4
votes
3
answers
171
views
3
answers
... 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 Boyer • 870
• updated
4 days ago by
genomax ♦ 60k
0
votes
1
answer
2.4k
views
1
answers
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 Boyer • 870
1
vote
0
answers
5.8k
views
0
answers
... 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 Boyer • 870
0
votes
1
answer
2.4k
views
1
answers
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 Boyer • 870
1
vote
0
answers
5.8k
views
0
answers
... 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 Boyer • 870
0
votes
1
answer
234
views
1
answers
... The hype is real o_o ...
written 9 weeks ago by
Roxane Boyer • 870
0
votes
1
answer
234
views
1
answers
... I see ;) Bacterial genome with 15000X for the win o/ ...
written 9 weeks ago by
Roxane Boyer • 870
0
votes
1
answer
234
views
1
answers
... "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 Boyer • 870
3
votes
1
answer
234
views
1
answer
... 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 ...
written 9 weeks ago by
Roxane Boyer • 870
• updated
9 weeks ago by
WouterDeCoster ♦ 35k
0
votes
0
answers
204
views
0
answers
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 Boyer • 870
Latest awards to Roxane Boyer
Popular Question
1 day ago,
created a question with more than 1,000 views.
For Canu assembler : meryl failed after 2 attempts
Popular Question
1 day ago,
created a question with more than 1,000 views.
For Canu assembler : meryl failed after 2 attempts
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 ?
Popular Question
7 weeks ago,
created a question with more than 1,000 views.
For Canu assembler : meryl failed after 2 attempts
Great Question
7 weeks ago,
created a question with more than 5,000 views.
For Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
Popular Question
7 weeks ago,
created a question with more than 1,000 views.
For Canu assembler : meryl failed after 2 attempts
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 ?
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Canu assembler : meryl failed after 2 attempts
Voter
5 months ago,
voted more than 100 times.
Popular Question
5 months ago,
created a question with more than 1,000 views.
For First time using maker
Prophet
6 months ago,
created a post with more than 20 followers.
For Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
Popular Question
6 months ago,
created a question with more than 1,000 views.
For First time using maker
Scholar
6 months ago,
created an answer that has been accepted.
For A: Polishing PacBio assembly : The ideal coverage for higly polymorphic species
Appreciated
8 months ago,
created a post with more than 5 votes.
For A: What can I do after my Pacbio genome assembly ?
Popular Question
8 months ago,
created a question with more than 1,000 views.
For First time using maker
Popular Question
8 months ago,
created a question with more than 1,000 views.
For First time using maker
Popular Question
8 months ago,
created a question with more than 1,000 views.
For What are the ".bax.h5" files generated by PacBio long reads sequencing ?
Autobiographer
9 months ago,
has more than 80 characters in the information field of the user's profile.
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 ?
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: What can I do after my Pacbio genome assembly ?
Popular Question
13 months ago,
created a question with more than 1,000 views.
For First time using maker
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
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1728 users visited in the last hour