User: Gautier Richard

gravatar for Gautier Richard
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340
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Location:
MPI IE, Freiburg, Germany
Website:
https://www.linkedin.c...
Twitter:
Gautier_Rich4rd
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Google Scholar Page
Last seen:
1 month, 3 weeks ago
Joined:
2 years ago
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Posts by Gautier Richard

<prev • 36 results • page 1 of 4 • next >
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Comment: C: RPKM and TPM when operating with small group of genes: is there a bias?
... EDIT#1 seems more reasonable than EDIT#2 depending on your experimental plan, i.e. if you want to perform comparisons in one genome between multiple conditions, a normalized expression level would be much more reliable than raw sequencing depth for a given gene. Imagine that your sequencing depth is ...
written 3 months ago by Gautier Richard340
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Comment: C: RPKM and TPM when operating with small group of genes: is there a bias?
... I don't think that RPKM or TPM are meant to be calculated for a handful of genes, you need to compute them genome-wide and keep the same values after subsetting genes. ...
written 3 months ago by Gautier Richard340
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Comment: C: Deeptools correlation plot: between RNAseq and H3K27ac ChIPseq
... I would recommend to call H3K27ac peaks, get nearest/overlapping genes with bedtools nearest, and plot the peaks maximum value alongside the associated genes expression with R / Python / Excel. Otherwise, rank genes from the most expressed to the least expressed and make a heatmap with deepTools p ...
written 3 months ago by Gautier Richard340
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Answer: A: DMR detection tools for whole genome bisulphite sequencing data in Plants
... I'm performing WGBS data analysis in plants using the Snakepipes WGBS pipeline. It uses *bwa-meth* for the mapping, *MethylDackel* to get the methylation levels and mbias correction and *metilene* to get the DMRs. - https://snakepipes.readthedocs.io/en/latest/content/workflows/WGBS.html - htt ...
written 3 months ago by Gautier Richard340
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Answer: A: data format for ggupset
... According to your question, I guess that you want to count the number of DEGs in common between your 8 conditions with UpSetR since it would be a nightmare with Venn Diagrams. You don't need ggupset for that, UpSetR might be a better solution since data preparation is much more straightforward. Mor ...
written 3 months ago by Gautier Richard340
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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 22 months ago by Gautier Richard340
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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 23 months ago by Gautier Richard340
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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 23 months ago by Gautier Richard340
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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 23 months ago by Gautier Richard340
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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 23 months ago by Gautier Richard340

Latest awards to Gautier Richard

Scholar 3 months ago, created an answer that has been accepted. For A: R for loop
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: R for loop
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: R for loop
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: R for loop
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Commentator 23 months ago, created a comment with at least 3 up-votes. For C: juicer.sh problem !
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: R for loop
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Scholar 24 months ago, created an answer that has been accepted. For A: R for loop
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