User: enxxx23

gravatar for enxxx23
enxxx23210
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European Union
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4 years, 9 months ago
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Posts by enxxx23

<prev • 45 results • page 1 of 5 • next >
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Comment: C: Tophat problem - R1 and R2 reads mapped to different strandeds of viral genome
... I totally agree! Do not use TopHat(2)! ...
written 10 weeks ago by enxxx23210
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Answer: A: RNA-Seq time-series analysis among disease samples - analysis strategy advice
... It would be great to have more info here, like for example: - number of replicates, - info about the times points (e.g. before and after the treatment time points?) - type of disease: cancer or non-cancer - tissues of origin for the samples (are all from the same tissue?), - is there healthy tissue ...
written 10 weeks ago by enxxx23210
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Comment: C: Best tool for variant calling
... I concurr. This is my experience too. What version of samtools are you using? ...
written 10 weeks ago by enxxx23210
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Answer: A: chimeric transcripts detection tool
... FusionCatcher https://sourceforge.net/projects/fusioncatcher/ ...
written 3 months ago by enxxx23210
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Answer: A: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
... I would answer like this to non-bioinformatician or non-statistician. EdgeR, DESeq2, Limma, and so on are different methods (which use complex statistics) and therefore one would expect when using different methods to get different results. Indeed there is some similarity at general/conceptual leve ...
written 3 months ago by enxxx23210
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Comment: A: Gene Set Enrichment Analysis after DESeq2
... I like DESeq2. It would be great to have in the future something like ROAST/CAMERA/GSEA in DESeq2 too! ...
written 3 months ago by enxxx23210
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Comment: C: Evaluate single cell data to look at combinations of gene expression within sing
... Using WGCNA requires at least 20 samples. Also WGCNA analysis is not "stable", which means that the another researcher will find impossible to reproduce the results of WGCNA analysis without having the original script where the WGCNA analysis was done. Also at a close inspection it looks like may mo ...
written 3 months ago by enxxx23210
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Comment: C: RNAseq with quantseq
... I meant that is there any reference (e.g. scientific article and not markerting material) which supports this? Do the authors of edger, limma, or DESeq2 concur with this? ...
written 18 months ago by enxxx23210
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Comment: C: RNAseq with quantseq
... Does R packages like edgeR, limma, DESeq2 work with QuantSeq 3' RNAseq? I mean, has anybody used and published results based on QuantSeq data analyzed with edgeR, limma, DESeq2? ...
written 18 months ago by enxxx23210
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Comment: C: Gene Fusion Detection: Rna-Seq Data
... Actually, Tophat-fusion and STAR-fusion need a lot of improvement. Tophat-fusion consistently in is the bottom of all comparisons of fusion finders. TopHat-fusion calls hundreds of thousands of fusions per sample when it is well known that fusions are very rare and one has one fusion for every 10 sa ...
written 22 months ago by enxxx23210

Latest awards to enxxx23

Popular Question 10 months ago, created a question with more than 1,000 views. For Public RNA-seq dataset for human & 2x250bp or longer
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: The new era of bioinformatics: simple and fast tools, fewer and more informative
Commentator 4.2 years ago, created a comment with at least 3 up-votes. For C: Genomics is not Special. Computational Biologists are reinventing the wheel for

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