User: Roxane Boyer
Roxane Boyer • 890
- Reputation:
- 890
- Status:
- Trusted
- Location:
- France / Toulouse / GeT-Plage
- Last seen:
- an hour ago
- Joined:
- 2 years, 8 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
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... Hi Benoit !
Nope, in the end I had some others projects I had to finish before this one, so I did not had any time to think about this... So you won't be reinventing the wheel ; )
I'll be very interested to test it if you are going to work on that !
Cheers,
Roxane ...
written 4 weeks ago by
Roxane Boyer • 890
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... 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 9 weeks ago by
Roxane Boyer • 890
• updated
9 weeks ago by
genomax ♦ 63k
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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 9 weeks ago by
Roxane Boyer • 890
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... 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 3 months ago by
Roxane Boyer • 890
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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 3 months ago by
Roxane Boyer • 890
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... 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 3 months ago by
Roxane Boyer • 890
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... The hype is real o_o ...
written 4 months ago by
Roxane Boyer • 890
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... I see ;) Bacterial genome with 15000X for the win o/ ...
written 4 months ago by
Roxane Boyer • 890
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... "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 4 months ago by
Roxane Boyer • 890
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... 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 4 months ago by
Roxane Boyer • 890
• updated
4 months ago by
WouterDeCoster ♦ 37k
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