User: Roxane Boyer

gravatar for Roxane Boyer
Roxane Boyer310
Reputation:
310
Status:
Trusted
Location:
France/Marseille/IBDM
Last seen:
2 days, 9 hours ago
Joined:
1 year, 2 months ago
Email:
r*************@gmail.com

Posts by Roxane Boyer

<prev • 143 results • page 1 of 15 • next >
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Comment: C: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... You're welcome ! Glad it could help :) ...
written 4 days ago by Roxane Boyer310
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Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
... This tutorial addresses to anyone in possession of PacBio sequencing data. After struggling myself to find and test appropriated tools, learning PacBio specific format, asking for precisions to kind PacBio guys, I've managed to gather a lot of useful informations that everyone may need in order to p ...
pbalign tutorial polishing pacbio arrow smrt limk written 5 days ago by Roxane Boyer310 • updated 1 day ago by bhagyathimmappa0
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Comment: C: Assembling PacBio reads using a reference genome
... I don't really understand why you are trying to guide your assembly with a reference. My guess is that you already tried a first de novo assembly, without any reference, and that you were skeptical about the results, as you said you want a reference to resolve ambiguities. What kind of ambiguities ...
written 10 days ago by Roxane Boyer310
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Missing file for RepeatModeler installation
... Hello everyone, I've been looking unsuccessfully for a library file which is necessary to run RepeatModeler. The file is named **RepeatPeps.lib**, it is supposed to come from RepeatMasker, but even after downloading it again and re install it, this file never show up. I've subscribed to giri datab ...
repeatmodeler repeatmasker written 24 days ago by Roxane Boyer310
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Comment: C: Substitution error rate and indel error rate from BAM file
... Actually, I was thinking about indelhist=, but I think I should convert my bam file inton a sam 1.4+, I guess that the actual version of samtools is outputting in this format ! ...
written 24 days ago by Roxane Boyer310
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Comment: C: Substitution error rate and indel error rate from BAM file
... Hi Brian ! I'm actually trying to use reformat.sh from bbmap suit to calculate the indel rate from a bam file. I've tried to launch it this way : ./reformat.sh in='assemblyVSIlluna-sorted.bam' out='assemblyVSIllumina-indels.txt' But the output generated is in fastq format. There is a lot o ...
written 24 days ago by Roxane Boyer310
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Comment: C: Tool for manual annotation curation
... I never worked with Artemis, and before downloading and installing he tool, I wanted to be sure it could be done. I was reading the Artemis description, but didn't saw anything about manual genome curation. ...
written 26 days ago by Roxane Boyer310
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Answer: A: Cufflinks stuck in processing locus
... Hi there, I actually faced the same issue month ago, I reported the issue here in github : https://github.com/cole-trapnell-lab/cufflinks/issues/72 but as you can see, the issue is still unsolved... As an alternative, I will suggest to use Stringtie : https://ccb.jhu.edu/software/stringtie/ It i ...
written 26 days ago by Roxane Boyer310
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Tool for manual annotation curation
... Hello everyone, I am looking for a visualization tool that will allow me to load different kind of features (a genome.fasta file, a annotation.gff/gtf file, bam an sam files...) but also to manually correct the annotation feature. For example, if I see a gene structure that is not concordant with ...
annotation tool written 26 days ago by Roxane Boyer310
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Comment: C: Interpreting coverage gaps when aligning Illumina reads against PacBio assembly
... My overall deletion rate is like 0.00026 and insertion rate is 0.00068 per base. This is really high, and I'm not sure I should annotate a sequence with so many indels. But I'm not sure about the meaning of this high rate. Could it be "simply" the reflect of an high polymorphism degree within this s ...
written 4 weeks ago by Roxane Boyer310

Latest awards to Roxane Boyer

Good Answer 7 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 5 months ago, created a question with more than 1,000 views. For Training Augustus for Maker
Appreciated 6 months ago, created a post with more than 5 votes. For A: What can I do after my Pacbio genome assembly ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What can I do after my Pacbio genome assembly ?
Centurion 6 months ago, created 100 posts.
Scholar 8 months ago, created an answer that has been accepted. For A: Trouble with Pilon installation
Rising Star 13 months ago, created 50 posts within first three months of joining.
Supporter 13 months ago, voted at least 25 times.

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