User: Roxane Boyer

gravatar for Roxane Boyer
Roxane Boyer110
Reputation:
110
Status:
Trusted
Location:
France/Marseille/IBDM
Last seen:
1 day, 19 hours ago
Joined:
8 months ago
Email:
r*************@gmail.com

Posts by Roxane Boyer

<prev • 91 results • page 1 of 10 • next >
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Answer: A: Choosing de novo genome assembly
... Hi ! I have also performed genome assembly using PacBio data and Canu assembler, and I was really satisfied of it. If you want to try something else, you can try Falcon assembler, proposed by PacificBiosciences ( https://github.com/PacificBiosciences/FALCON ). Falcon is aiming to output a diploid ...
written 1 day ago by Roxane Boyer110
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Comment: C: Aligning very short and paired Illumina reads
... Oh this is interesting, so how did you detected this problem ? IS FastQC enough to detect such an issue ? How did you solved it ? ...
written 24 days ago by Roxane Boyer110
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Comment: C: Aligning very short and paired Illumina reads
... Okay, thanks for your fast reply. Do you think it will be suited for very short reads like mines ? ...
written 24 days ago by Roxane Boyer110
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Aligning very short and paired Illumina reads
... Hi everyone, I faced a issue using bwa for some very shorts reads I have (49bp). I have numerous paired Illumina reads that I want to align against an assembly I made. I saw this previous post about paired-reads aligning with several files : https://www.biostars.org/p/134395/ , which propose to us ...
genome illumina alignement written 24 days ago by Roxane Boyer110
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Answer: A: Trouble with Pilon installation
... I allow myself to add my own answer to this question, in case some other people wonder. So, clone the deposit is probably not the way we should install Pilon. I've ran successfully Pilon after directly the .jar file available here : https://github.com/broadinstitute/pilon/releases and then typing ...
written 4 weeks ago by Roxane Boyer110
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Trouble with Pilon installation
... Hello everyone ! I'm trying to polish my genome assembly, and for this I need to use Pilon (there other options from PacBio tools and software being unavailable). My problem is that I don't see anywhere some recommendations to install this tool. I read the several sections form the wiki page : htt ...
pilon installation polishing written 4 weeks ago by Roxane Boyer110
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Comment: C: Alternative to BLASR ?
... Hi Genomax, I'm coming back to you again about BBmap. After having some issues with bwa-mem (depending on the number of threads used, I didn't get the same results), I want to try bbmap. I understood that the large reads from my pacbio sequencing will have to be sliced in smaller pieces. However, a ...
written 4 weeks ago by Roxane Boyer110
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Group a set of plots using MUMmer
... Hello everyone ! This is my first try using MUMmer, I would like to visualize something close to this publication : http://biorxiv.org/content/biorxiv/early/2016/12/02/090969.full.pdf (page 18). I'm trying to align the 6 longest contigs of my assembly to see where it aligns on D.melanogaster genome ...
mummer-plot mummer alignment written 5 weeks ago by Roxane Boyer110 • updated 5 weeks ago by skbrimer330
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Comment: C: BWA-MEM using long PacBio reads
... Well, me and some other people are encountering the same problem with blasr. Just look at this issue in github : https://github.com/PacificBiosciences/blasr/issues/324 It indeed seems that it accept only "valid" (whatever it means...) input files. Even if my files come directly from PacBio tools, I' ...
written 5 weeks ago by Roxane Boyer110
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Comment: C: TPM Transcript per Million : Formula
... When I was confused with the different quantification measures, I used to read documentations of this site : https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/ I hope it could help you a bit with your reflexion ! Woups just saw that you already read ...
written 5 weeks ago by Roxane Boyer110

Latest awards to Roxane Boyer

Scholar 4 weeks ago, created an answer that has been accepted. For A: Trouble with Pilon installation
Rising Star 6 months ago, created 50 posts within first three months of joining.
Supporter 6 months ago, voted at least 25 times.

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