User: Roxane Boyer
Roxane Boyer • 510
- Reputation:
- 510
- Status:
- Trusted
- Location:
- Auvergne
- Last seen:
- 11 hours ago
- Joined:
- 1 year, 10 months ago
- Email:
- r*************@gmail.com
After working 1.5 years at the Institute of Developmental Biology of Marseille on RNAseq data and genome assembly with PacBio data, I'm currently looking for a new job accross the world. I would really like to continue working on long read assembly using technologies such as PacBio or Oxford Nanopore.
Posts by Roxane Boyer
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... Hi Eric! To polish my assembly, I've used the Pacino polishing tool which is quiver. ...
written 27 days ago by
Roxane Boyer • 510
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... Hello ! Well, I never did such a thing yet, I don't have any idea of how to do it, I'm sorry. ...
written 3 months ago by
Roxane Boyer • 510
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... Hello everyone !
I'm trying to test out Breakdancer, a tool to detect strucural variantion in a alignement ,that first require to run a perl tool which create a config file using your bam file.
I used the tool this way on a merged bam :
Loutre:~/breakdancer/perl$ ./bam2cfg.pl '/media/loutre/ ...
written 3 months ago by
Roxane Boyer • 510
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... It appears that one of my gff was in fact a gtf... Probably I mistake I made while using stringtie output. Problem solved now. Than you for your help ! ...
written 5 months ago by
Roxane Boyer • 510
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... Hm your guess was right. Deactivating augustus did not changed theses errors. I got exactly the same message. I guess something is wrong with one of my input files. ...
written 5 months ago by
Roxane Boyer • 510
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... As you adviced me in a previous post, I specified it using augustus_species=fly. I downloaded a fly data set of augustus on thei website, so the set is already trained and ready. It didnt showed off any errors concerning augustus. ...
written 5 months ago by
Roxane Boyer • 510
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... Yes I'm pretty sure, there is no redundancy. It's the same file I've worked with since the begining. I used it for maker without Augustus. And it was working just fine before. Adding augustus input in the only thing I changed ...
written 5 months ago by
Roxane Boyer • 510
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... You have an example of name just right above here : Andromeda.
Here some others example of contig names that failed : Draco, Cepheus, Gemini, Contig_5, etc...
Some contigs (a few) succeeded to be annotated. For example Contig_534 etc... Only small contigs. ...
written 5 months ago by
Roxane Boyer • 510
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... Hello everyone,
I'm using maker since a while now, and I never got any issues about it. I recently tried to include some Augustus prediction inside the annotation process by changing the line : `augustus_species=fly` as it was specified in some maker tutorial.
At the end of the process, only a doz ...
written 5 months ago by
Roxane Boyer • 510
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... Dear Zusman,
> If i am not mistaken, bas.h5 file only contains the quality
> information for the reads. So, for analysis we require .bax.h5 files.
> Also each .bax.h5 files correspond to different sample.
Everything you said is correct so far.
> Also each .bax.h5 files correspond to d ...
written 6 months ago by
Roxane Boyer • 510
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