User: Thibault D.

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Thibault D.510
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510
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Location:
European Union
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9 hours ago
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4 years, 6 months ago
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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 13 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 13 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 15 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 15 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 18 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 20 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 20 months ago by Thibault D.510 • updated 10 weeks ago by Biostar ♦♦ 20
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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 21 months ago by Thibault D.510 • updated 3 days ago by vincent.lacroix100
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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 2.1 years 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 2.8 years ago by Thibault D.510

Latest awards to Thibault D.

Popular Question 9 weeks ago, created a question with more than 1,000 views. For Understanding MMDiff output files
Popular Question 10 months ago, created a question with more than 1,000 views. For Understanding MMDiff output files
Popular Question 13 months ago, created a question with more than 1,000 views. For Understanding MMDiff output files
Popular Question 15 months ago, created a question with more than 1,000 views. For Why does TopHat return wrong XS-Strand attribute in BAM ?
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: building index with HISAT2
Scholar 15 months ago, created an answer that has been accepted. For A: Bowtie2 reporting alignments count
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Cuffmerge or Cuffcompare?!
Appreciated 24 months ago, created a post with more than 5 votes. For A: Cuffmerge or Cuffcompare?!
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Bowtie2 vs Tophat Whats the difference
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Cuffmerge or Cuffcompare?!
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Why does TopHat return wrong XS-Strand attribute in BAM ?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Scholar 3.7 years ago, created an answer that has been accepted. For A: Bowtie2 reporting alignments count
Supporter 3.7 years ago, voted at least 25 times.
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Teacher 4.1 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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