User: Thibault D.

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Thibault D.510
Reputation:
510
Status:
Trusted
Location:
European Union
Last seen:
3 days, 2 hours ago
Joined:
3 years, 8 months ago
Email:
t**************@outlook.fr

Posts by Thibault D.

<prev • 54 results • page 1 of 6 • next >
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Comment: C: SARTools and batch effects
... Hi, as far as I read the doc, I think you can provide multiple columns and use a R-formula to give a more complex design to SARTools. Remember, it depends on the tool you're using within SARTools (DESeq2 or EdgeR). You may have to refer to their own documentations. ...
written 3 months ago by Thibault D.510
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Answer: A: STAR alignment command.
... Hi, It is not necessary, but the default value is 1 thread. In my experience, with human genomic data, increasing the number of threads above 10 is not very valuable. In any case, the number of threads just speeds up the process. It will **not** change your results, just the time you'll have to wa ...
written 3 months ago by Thibault D.510
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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 5 months ago by Thibault D.510
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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 5 months ago by Thibault D.510
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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 8 months ago by Thibault D.510
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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 9 months ago by Thibault D.510
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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 9 months ago by Thibault D.510 • updated 9 months ago by Devon Ryan84k
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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 11 months ago by Thibault D.510 • updated 9 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 15 months ago by Thibault D.510
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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 24 months ago by Thibault D.510

Latest awards to Thibault D.

Popular Question 3 months ago, created a question with more than 1,000 views. For Understanding MMDiff output files
Popular Question 4 months ago, created a question with more than 1,000 views. For Why does TopHat return wrong XS-Strand attribute in BAM ?
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: building index with HISAT2
Scholar 5 months ago, created an answer that has been accepted. For A: Bowtie2 reporting alignments count
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Cuffmerge or Cuffcompare?!
Appreciated 13 months ago, created a post with more than 5 votes. For A: Cuffmerge or Cuffcompare?!
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Bowtie2 vs Tophat Whats the difference
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: Cuffmerge or Cuffcompare?!
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Why does TopHat return wrong XS-Strand attribute in BAM ?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Scholar 2.8 years ago, created an answer that has been accepted. For A: Bowtie2 reporting alignments count
Supporter 2.9 years ago, voted at least 25 times.
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Teacher 3.2 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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