User: Thibault D.

gravatar for Thibault D.
Thibault D.500
Reputation:
500
Status:
Trusted
Location:
European Union
Last seen:
3 days, 14 hours ago
Joined:
3 years, 4 months ago
Email:
t**************@outlook.fr

Posts by Thibault D.

<prev • 52 results • page 1 of 6 • next >
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Comment: C: building index with HISAT2
... I indeed made a mistake as I did not red the Hisat2 doc before answering. Hisat2 expects a comma-separated list of file, and my previous answer was a space-separated list of files. That is why the previous command produced many references. Parameters expansion with curly brackets produces a *space- ...
written 4 weeks ago by Thibault D.500
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Answer: A: building index with HISAT2
... Hi, You're missing one thing with your parameter expansion in bash. Try the following commnd line: ./hisat2-build /data/memona/reference/{1.fa,2.fa,3.fa,4.fa,5.fa,6.fa,7.fa,8.fa,9.fa,10.fa,11.fa,12.fa,13.fa} hisat_index It should be better, as I think all your fasta files are in the reference ...
written 4 weeks ago by Thibault D.500
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Answer: A: Python script error
... Hi, The python error is clear: the syntax is not correct. Let's see your line. You have a lonely parenthesis on your print. Try this: print str( entry.id ) Instead of: print strentry.id) This is a syntax error. ...
written 4 months ago by Thibault D.500
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Comment: C: In simple words - what is k-mer??
... You do know many specific k-mers: an **hexamer** is a k-mer of length 6, a **dimer** is a k-mer of length 2. Etc. ...
written 6 months ago by Thibault D.500
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R formula in RNA-Seq differential analysis with multiple parameters
... Dear all, I'm working on differential genes/transcripts analysis in which I am interested in the effect of a treatment between patients, and their reaction across two age groups. I have a large number of patients in that study. Here, both age and treatment factors are interesting. However, I am ex ...
R sleuth deseq2 rna-seq statistics written 6 months ago by Thibault D.500 • updated 6 months ago by Devon Ryan79k
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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 7 months ago by Thibault D.500 • updated 5 months ago by Biostar ♦♦ 20
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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 11 months ago by Thibault D.500
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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 20 months ago by Thibault D.500
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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 20 months ago by Thibault D.500
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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 2.1 years ago by Thibault D.500

Latest awards to Thibault D.

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Why does TopHat return wrong XS-Strand attribute in BAM ?
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: building index with HISAT2
Scholar 4 weeks ago, created an answer that has been accepted. For A: Bowtie2 reporting alignments count
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Cuffmerge or Cuffcompare?!
Appreciated 9 months ago, created a post with more than 5 votes. For A: Cuffmerge or Cuffcompare?!
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Bowtie2 vs Tophat Whats the difference
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Appreciated 24 months ago, created a post with more than 5 votes. For A: Cuffmerge or Cuffcompare?!
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Why does TopHat return wrong XS-Strand attribute in BAM ?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Scholar 2.5 years ago, created an answer that has been accepted. For A: Bowtie2 reporting alignments count
Supporter 2.5 years ago, voted at least 25 times.
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Teacher 2.9 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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