User: kristoffer.vittingseerup

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Posts by kristoffer.vittingseerup

<prev • 65 results • page 1 of 7 • next >
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Answer: A: How does Cufflinks DE calculate q-value?
... If you want to recalculate anything you should do it based on the (estimated) count values since they contain the read-count uncertainty (much higher for 3 reads than 300 reads) - somthing you normalize away when you calculate FPKM. ...
written 10 days ago by kristoffer.vittingseerup350
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Answer: A: How to find common alternative splicing events or novel transcripts among differ
... The pipeline Kevin suggest will give you the basis for doing the downstream analysis of acutal splice events. If you are interested in isoform switches (which enables easy biological interpretation) you can use one of my tool [IsoformSwitchAnalyzeR][1]. Alternatively [rMATS][2] or [DEXSeq][3] can b ...
written 10 days ago by kristoffer.vittingseerup350
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Answer: A: Coordinates for Transcription Start Site (TSS)
... The problem is there is no good definition of which TSS to use from a specific gene - I'm guessing for release 74 Ensemble simply reported the most upstream - but our research shows that is not a good proxy for the most used (only in ~50% of cases). I think you might be better of with using the [FA ...
written 10 days ago by kristoffer.vittingseerup350
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Answer: A: A Theoretical Question About RNA-Seq Normalization
... I would do option no 1 since else you are letting the 30 libraries without genotype data affect the normalisation - although I doubt it have a huge impact with the number of samples you are analysing. ...
written 17 days ago by kristoffer.vittingseerup350
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Comment: C: ActiveEnhancers and Gene expression
... I would be very carefull with this. When analysing different types of chromatin interaction data just talking the nearest gene is only slightly better than randomly selecting genes (AUROC values in the 0.5-0.6 range) - see fx fig 3b-e in [this recent article][1]. [1]: https://www.nature.com/arti ...
written 21 days ago by kristoffer.vittingseerup350
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Comment: C: ActiveEnhancers and Gene expression
... To help you out I need to know which cell type and organisme are you working with? ...
written 21 days ago by kristoffer.vittingseerup350
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Answer: A: exon skipping and RNA-Seq
... If you are more interested in isoform switches - where you can acutally start predicting the consequences - you should take a look at my tool [IsoformSwitchAnalyzeR][1] which can help you identification and analysis of isoform switches with predicted functional consequences (such as gain/loss of pro ...
written 21 days ago by kristoffer.vittingseerup350
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Comment: C: exon skipping and RNA-Seq
... Did you try rMATS v4.0.1 or higher? (They made some large updates there). ...
written 21 days ago by kristoffer.vittingseerup350
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Answer: A: Plotting TSS & TTS for Chip-seq peaks
... Alternative you could just calculate and visualise the distances yourself. The distances can easily be found with [GenomicRanges][1] in R. [1]: http://bioconductor.org/packages/devel/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesIntroduction.pdf ...
written 6 weeks ago by kristoffer.vittingseerup350
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Comment: C: Best tools for Visualing RNASeq data
... Why not simply a violin plot log2 fold chages for all genes in that pathway? ...
written 6 weeks ago by kristoffer.vittingseerup350

Latest awards to kristoffer.vittingseerup

Scholar 8 weeks ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Scholar 3 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Scholar 5 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: RNA-seq analysis between 2 closely related strains of the same species

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