User: Gautier Richard

gravatar for Gautier Richard
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MPI IE, Freiburg, Germany
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https://www.linkedin.c...
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1 month, 1 week ago
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Posts by Gautier Richard

<prev • 31 results • page 1 of 4 • next >
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Comment: C: "bowtie2 died with signal 9 (KILL)" error message, having trouble figuring out h
... Yes you can try using BWA for ungapped mapping. If you think that your alignments might have gaps, please use STAR (it could as you are analysing transcripts right?). ...
written 3 months ago by Gautier Richard280
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Answer: A: What tool can be used to predct regulatory element within an input sequence ?
... Your best chance is to use FIMO from the MEME suite and compare your sequence to the Chicken DNA Binding Protein Motifs Databases. http://meme-suite.org/doc/fimo.html I recommend using a Galaxy version of FIMO if you are not familiar with command-line tools. One issue is that MEME doesn't have a ...
written 3 months ago by Gautier Richard280
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Comment: C: Remove duplicates in an extremely large text file
... If you sort first I guess the chance is very small no? ...
written 4 months ago by Gautier Richard280
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Comment: C: "bowtie2 died with signal 9 (KILL)" error message, having trouble figuring out h
... I think it is a good way. Just ask how to increase the memory amount allowed to your job to your local bioinformaticians / cluster (HPC) managers. With the **Slurm** job manager (sbatch or SlurmEasy to launch scripts) this can be easily done at the beginning of the shell script you use to launch bow ...
written 4 months ago by Gautier Richard280
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Comment: C: "bowtie2 died with signal 9 (KILL)" error message, having trouble figuring out h
... It seems that you run out of memory. ...
written 4 months ago by Gautier Richard280
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Comment: C: RNA-Seq Differential gene expression
... Following this link you'll find a paper explaining how to use EdgeR and how to properly set a contrast matrix that will help you making the correct comparisons: https://f1000research.com/articles/5-1408/v3 If you don't do KO1 vs KO2 or KO2 vs OE1 comparisons, perhaps it is better to only consider ...
written 4 months ago by Gautier Richard280
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Comment: C: How to plot gene cluster
... IGV should do the trick no? Are these sequences next to each other? If not, you can rely on pyGenomeTracks to plot each sequence next to each other in a nice and automated manner: https://github.com/deeptools/pyGenomeTracks Otherwise, you can use illustrator or Inkscape if you want to just do it f ...
written 4 months ago by Gautier Richard280
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Comment: C: Calculating TPM from featureCounts output
... Fragment Length usually corresponds to the size of the DNA or RNA fragments that have been sequenced. Such information is usually obtained with a Bioanalyzer. It can also be infered from the distance between pairs when performing paired-end sequencing. ...
written 4 months ago by Gautier Richard280
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Answer: A: Per-base coverage to bedgraph or bigwig
... Per base bedgraph should be of the following format: Chr1 0 1 0.846 Chr1 1 2 0.745 Chr1 2 3 0.433 Chr1 3 4 0.313 Then you can convert it to bigwig easily using `bedGraphToBigWig` from UCSCTools. Having your "custom file" should help us to guide you about how to get the bedgraph ...
written 4 months ago by Gautier Richard280
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Comment: C: Analysis pipeline for 3e Hi-C
... The idea might be to increase the resolution of Restriction Fragment length binned Hi-C matrices. More restriction sites = smaller bins = higher resolution. I don't know if it helps them to identify new features though. ...
written 4 months ago by Gautier Richard280

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Teacher 3 months ago, created an answer with at least 3 up-votes. For A: R for loop
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