User: Thibault D.

gravatar for Thibault D.
Thibault D.430
Reputation:
430
Status:
Trusted
Location:
European Union
Last seen:
2 days, 4 hours ago
Joined:
2 years, 9 months ago
Email:
t**************@outlook.fr

Posts by Thibault D.

<prev • 47 results • page 1 of 5 • next >
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Kissplice2refgenome does not handle # in the very begining of GTF files
... Hi, I've been using Kissplice pipeline lately to perform personnal RNASeq analysis. As I used the pipeline described in the official Kissplice documentation, I've come across an error. With the following command line: kissplice2refgenome-1.0.0/kissplice2refgenome -a genomeDir/gencode.v24.chr_ ...
gtf rna-seq kissplice written 16 days ago by Thibault D.430
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Answer: A: How to add new operation terms to EDAM ontology
... Hi, You may open a new topic on the [Github][1] page. [1]: https://github.com/edamontology/edamontology/issues ...
written 4 months ago by Thibault D.430
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Comment: C: Volcano plot from Posterior probabilities instead of p-value
... If I do not multiply by -1, the volcano plot with PP would be reversed horizontally: the maximum value would be 0, the worst PP ...
written 12 months ago by Thibault D.430
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Volcano plot from Posterior probabilities instead of p-value
... Hi ! I'm currently diving into isoforms differential expression analysis results. I use the duo RSem-EBSeq to perform this work. I'd like to build a volcano plot of my data. RSem-EBseq returns posterior probabilities (PP) and no p-values (PV) at all. I am aware, that both PP and PV allows me to an ...
volcano plots posterior probability statistics written 12 months ago by Thibault D.430
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Comment: C: differential gene expression using sleuth
... I don't think so, I can not find anything within Sleuth to perform this kind of analysis. ...
written 18 months ago by Thibault D.430
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Comment: C: differential gene expression using sleuth
... I don't understand. Would you like to display your differential gene expression analysis with Sleuth style, or to perform this differential gene expression analysis with Sleuth, or ... ? ...
written 18 months ago by Thibault D.430
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Answer: A: differential gene expression using sleuth
... Hi, you can use [tximport][1], then [SARTools][2] to do such analysis. Please note, that the next DESeq2 update will include tximport as a function. Thibault [1]: https://github.com/mikelove/tximport [2]: https://github.com/PF2-pasteur-fr/SARTools ...
written 19 months ago by Thibault D.430
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Comment: C: RNAseq problems with tophat
... Hi clizama, Are you sure the error message you posted here is complete ? It seems truncated to me. Could we have the complete recording of tophat's logging, so that we'll be able to help you ? ...
written 19 months ago by Thibault D.430
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Answer: A: GFF3 file format
... Hi rakeshmbb, It is not written in GFF3 specifications, however most of the GFF3 files are sorted according to ascending position. This order "reverses" the features' order of genes present in the minus strand. ...
written 20 months ago by Thibault D.430
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Answer: A: Tool for simulating stranded RNA-Seq data
... Hi, Here are two of them : Polyester and FluxSimulator. They have different kind of parameters, Flux Simulator is "mathematics-oriented". Polyester is IMHO easier to use. ...
written 20 months ago by Thibault D.430

Latest awards to Thibault D.

Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Cuffmerge or Cuffcompare?!
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Bowtie2 vs Tophat Whats the difference
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Appreciated 16 months ago, created a post with more than 5 votes. For A: Cuffmerge or Cuffcompare?!
Popular Question 17 months ago, created a question with more than 1,000 views. For Why does TopHat return wrong XS-Strand attribute in BAM ?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Scholar 23 months ago, created an answer that has been accepted. For A: Bowtie2 reporting alignments count
Supporter 23 months ago, voted at least 25 times.
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types

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