Moderator: Nicolas Rosewick

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Posts by Nicolas Rosewick

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Comment: C: Expression of specific genes between tumor and normal
... normalized read count should be ok. Best would be to plot the results as a boxplot for example. check DESeq2 vignette for more information : https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#differential-expression-analysis ...
written 8 days ago by Nicolas Rosewick6.5k
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Comment: C: Expression of specific genes between tumor and normal
... Yes it is the same. You should always use all genes for the analysis. And then check the genes of interest. ...
written 8 days ago by Nicolas Rosewick6.5k
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Answer: A: Expression of specific genes between tumor and normal
... You should **always** performed analysis on all genes and then extract information concerning your genes of interest. DESeq or edgeR will use the information of all gene read count for the expression analysis. If you do not use all genes you will introduce big biais such as depth normalization. ...
written 8 days ago by Nicolas Rosewick6.5k
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Comment: C: Dummy / simulated genomic data
... I'll take a look. Thanks ...
written 9 days ago by Nicolas Rosewick6.5k
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Comment: C: Dummy / simulated genomic data
... No my account was not hacked. I know how to simulate genomic data but I do not want to reinvent the wheel if there is already some simulated datasets available ;) and no offense taken ;) ...
written 9 days ago by Nicolas Rosewick6.5k
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Dummy / simulated genomic data
... Hi, For some testing purpose I would like to use some dummy genomic data (VCF, BAM and FASTQ - for WGS, WES, RNA-Seq and gene panels). Before trying to simulate them I would like to know if there is such dataset already available somewhere ? Thank you ...
data simulated dummy written 9 days ago by Nicolas Rosewick6.5k
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Comment: C: Size of typical genomic data
... I took this information from https://www.biostars.org/p/47646/#47683 ...
written 9 weeks ago by Nicolas Rosewick6.5k
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Size of typical genomic data
... Hi, I'm preparing some slides and would like to have some uptodate information related to typical sizes of NGS applications (VCF and BAM) e.g. exome ; WGS ; RNA-Seq ; gene panels , etc... Looking in the litterature that's what I found (for 30x coverage and 2x100bp read length) Type of NGS ...
size genomic written 9 weeks ago by Nicolas Rosewick6.5k • updated 9 weeks ago by toralmanvar420
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Comment: C: Compute correlation for depth of coverage between 2 datasets with different leng
... I compute the mean value per genomic position. So you will end with two dataframes with the genomic position common to both original dataframes. Each position containing the mean of the DP values for this position. Thus not one value... ...
written 10 weeks ago by Nicolas Rosewick6.5k
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Comment: C: SAM CIGAR parsing and position counter in R
... What about insertion, deletion and splice junction encoded within CIGAR ? If I understand well you want to report all position where one read aligned. ...
written 10 weeks ago by Nicolas Rosewick6.5k

Latest awards to Nicolas Rosewick

Popular Question 5 days ago, created a question with more than 1,000 views. For Plot Alignment With Gviz
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Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
Scholar 10 weeks ago, created an answer that has been accepted. For C: How to increase cytoscape memory?
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Hierarchical Clustering And Heatmap Analysis For Rna-Seq Data
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