User: Roxane Boyer

gravatar for Roxane Boyer
Roxane Boyer430
Reputation:
430
Status:
Trusted
Location:
France/Marseille/IBDM
Last seen:
5 days, 9 hours ago
Joined:
1 year, 4 months ago
Email:
r*************@gmail.com

Posts by Roxane Boyer

<prev • 155 results • page 1 of 16 • next >
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Comment: C: Maker failure on almost all contig
... 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 16 days ago by Roxane Boyer430
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Comment: C: Maker failure on almost all contig
... 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 16 days ago by Roxane Boyer430
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Comment: C: Maker failure on almost all contig
... 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 17 days ago by Roxane Boyer430
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Comment: C: Maker failure on almost all contig
... 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 17 days ago by Roxane Boyer430
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Comment: C: Maker failure on almost all contig
... 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 17 days ago by Roxane Boyer430
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Maker failure on almost all contig
... 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 ...
software error annotation maker written 17 days ago by Roxane Boyer430
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Comment: C: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... 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 weeks ago by Roxane Boyer430
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Comment: C: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... Hi Kyungyong ! So I'm not really used to PacBio dataset with adaptaters, but I saw an option in the bam2bam tools from pacbio that allow to specify adaptaters and barcodes sequence. Maybe it allow a kind of filter to put apart adapaters form the output bam ? Here is the SMRT Tools Guide that may ...
written 6 weeks ago by Roxane Boyer430
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Comment: C: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... Thanks for that tip ! So when you create the dataset, you can specify the desired coverage for example ? ...
written 7 weeks ago by Roxane Boyer430
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Answer: A: Polishing PacBio assembly : The ideal coverage for higly polymorphic species
... After a few months working on my dataset, I think I finnally managed to give myself an answer. I'm reporting here my thought so it can benefit to anyone in need. My question was : **Which polishing coverage should I use to reduce fragmented and missing genes ?** In the past, I reported results for ...
written 7 weeks ago by Roxane Boyer430

Latest awards to Roxane Boyer

Popular Question 23 days ago, created a question with more than 1,000 views. For First time using maker
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: What can I do after my Pacbio genome assembly ?
Popular Question 4 weeks ago, created a question with more than 1,000 views. For First time using maker
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Training Augustus for Maker
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: What can I do after my Pacbio genome assembly ?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Trouble with Pilon installation
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: What can I do after my Pacbio genome assembly ?
Popular Question 7 months ago, created a question with more than 1,000 views. For Training Augustus for Maker
Appreciated 8 months ago, created a post with more than 5 votes. For A: What can I do after my Pacbio genome assembly ?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: What can I do after my Pacbio genome assembly ?
Centurion 8 months ago, created 100 posts.
Scholar 10 months ago, created an answer that has been accepted. For A: Trouble with Pilon installation
Rising Star 15 months ago, created 50 posts within first three months of joining.
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