User: kristoffer.vittingseerup

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Posts by kristoffer.vittingseerup

<prev • 46 results • page 1 of 5 • next >
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Answer: A: Alternative splicing: explanation about delta psi values
... I must admit I'm also a bit confused. Note sure how to interpret PSI values for isoforms (instead of an exon) since it have to be different than Isoform Fractions (as they are not summing to zero). You could take a look at [IsoformSwitchAnalyzeR][1] to see whether that does what you want. [1]: ...
written 3 days ago by kristoffer.vittingseerup290
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Comment: C: kal's test on rpkm vs raw counts
... Could you elaborate on what it is you actually want to do? Then we migth be better able to help you. ...
written 4 days ago by kristoffer.vittingseerup290
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Answer: A: SpliceR visualization tool
... Sound like you rather want to do is a sashimi plot - see fx the [IGV plugin][1] then using spliceR [1]: https://software.broadinstitute.org/software/igv/Sashimi ...
written 5 days ago by kristoffer.vittingseerup290
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Answer: A: Can spliceR be used to classify the AS events for denovo transcripts?
... Yep it can - it relies on comparing the (assembled) transcripts to one another. ...
written 5 days ago by kristoffer.vittingseerup290
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Answer: A: which option is better for DESeq2 analysis: salmon or htseq-count?
... I would definitively go for Salmon (or Kallisto) for three reasons: 1) Isoform/transcript based quantification can handle multi-mapping reads - which otherwise gives a bias in genes with less unique sequences - see [this][1] post. 2) Isoform/transcript based quantification tools such as Salmon and ...
written 5 days ago by kristoffer.vittingseerup290
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Answer: A: Stringtie and Cufflinks and Cuffmerge
... Yep. But if you look at the figures on https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual you seen they suggest to use stringtie -merge. ...
written 6 days ago by kristoffer.vittingseerup290
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Answer: A: Fantom5 enhancers to TSS_distance
... Unfortunatly I dont think you can - mostly because the "association" to an enhancer is not something that is clear how to best do. So you will have to first deside which enhancers and TSSs you define as associated and then the rest should be easy using fx GenomicRanges in R with the distance() func ...
written 5 weeks ago by kristoffer.vittingseerup290
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Answer: A: Enhancer distance cutoff
... That is a question we cannot answer as there is no max distance. We even know of enhancers that act on different chromosomes - but those are naturally rare events. From a more practical orientation a possible cold be features within the same TAD (topological associated domain) or features within +/ ...
written 5 weeks ago by kristoffer.vittingseerup290
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Comment: C: Differential Gene Expression Analysis using data_RNA_Seq_v2_expression_median RS
... Yes i suggest voom-limma because when you have many replicates (which you do in the TCGA data) they perform similar in benchmark. The difference then becomes that instead of waiting hours on edgeR or DESeq2 you can wait seconds/minuts on limma allowing much greater flexibility. ...
written 5 weeks ago by kristoffer.vittingseerup290
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Answer: A: Differential Gene Expression Analysis using data_RNA_Seq_v2_expression_median RS
... Hi Gokce Answers below 1) Yes you can you the log-transformation as you describe - but you could also use a smaller pseudo-count (say 0.01) punishing smaller changes less. 2) Raw count data from TCGA's RNA_Seq_V2 are available via the [CDC data portal][1] or a most of other APIs such as [TCGAbiol ...
written 6 weeks ago by kristoffer.vittingseerup290

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