User: kristoffer.vittingseerup

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Posts by kristoffer.vittingseerup

<prev • 458 results • page 1 of 46 • next >
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Answer: A: Merged vs. Ensembl GTF for htseq-count
... I've written a bit about such considerations [here][1] - hope this is helpfull. [1]: https://bioconductor.org/packages/devel/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR.html#what-quantification-tools-should-i-use ...
written 5 days ago by kristoffer.vittingseerup3.2k
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Answer: A: what should I do first: transciptome annotation or DE analysis?
... You definitively should remove contaminants before doing your DE analysis. Else you are just testing which sample have more contamination which again will bias your analysis making it untrustworthy. With regards to the number of differentially expressed features there are no guidelines - it depends ...
written 5 days ago by kristoffer.vittingseerup3.2k
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Comment: C: ERROR Cuffmerge for differential gene and expression analysis?
... Here is [a link][1] for a short description on what quantification options you have with RNASeq data. It all depends on your questions :-) [1]: https://bioconductor.org/packages/devel/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR.html#what-quantification-tools-should-i-use ...
written 18 days ago by kristoffer.vittingseerup3.2k
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Answer: C: Why 'filterByExpr' does not eliminate low read counts from the expression data?
... Before normalization (or acutally it does not matter as filterByExp does not consider the normalization since it filters on counts). What values do you have in the Ctrl1, Ctrl2, Str1 and Str2 coulmns? CPM? In that case the filtering probably works as gene1 have at least 0.657007 * Xe6 reads in two ...
written 18 days ago by kristoffer.vittingseerup3.2k
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Answer: A: cufflinks result interpretation
... Please note that if you want to compare the expression of the two samples you need to first run Cuffmerge and then requantify the samples on the joint transcriptome. You can read more at [cufflinks website][1] or [here][2]. [1]: http://cole-trapnell-lab.github.io/cufflinks/manual/ [2]: https:/ ...
written 29 days ago by kristoffer.vittingseerup3.2k
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Comment: C: cufflinks result interpretation
... Tophat(2) is outdated - Cufflinks is not...? ...
written 29 days ago by kristoffer.vittingseerup3.2k
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Comment: C: How to distinguish FPKM from TPM?
... From the numbers you can also tell that they are log transformed. ...
written 29 days ago by kristoffer.vittingseerup3.2k
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Comment: C: salmon TPM output to linear regression in R
... Plase also note that raw TPM values are not normal distributed so you should not use `lm` directly on them. Log2 transform them first (remember a pseudo count of your choice). ...
written 29 days ago by kristoffer.vittingseerup3.2k
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Comment: C: how to know the isoform length and exon number of particular gene from rna sampl
... Sorry but I do not understand what you want to do. Could you elaborate - and also please comment on why the nucleotide sequence in the fasta file is not good enougth? ...
written 29 days ago by kristoffer.vittingseerup3.2k
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Answer: A: how to know the isoform length and exon number of particular gene from rna sampl
... You simply look it up in the the annoation you used tu build the index for RSEM. If you used a fasta file you can look up the isoform length (as it is the same length as the number of nucleotides for that entry). If you want the number of exons you will have to download the corresponding GTF file an ...
written 4 weeks ago by kristoffer.vittingseerup3.2k

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Scholar 18 days ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
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