User: kristoffer.vittingseerup

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@kvittingseerup
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k***********************@bio.ku.dk

Posts by kristoffer.vittingseerup

<prev • 293 results • page 1 of 30 • next >
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Answer: A: Running prepare.py on remote server
... You can use the R package [tximport][1] specifically look at [this section of the vignette][2] (which also explain how to continue with DESeq2 analysis a bit further down). An alternative is the importIsoformExpression() function from my R package [IsoformSwitchAnalyzeR][3] which will enable you to ...
written 3 days ago by kristoffer.vittingseerup1.9k
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Comment: C: Error IsoformSwitchAnalyzeR with kallisto data and ensembl annotation gtf
... For R-3.5.1 you can get IsoformSwitchAnalyzeR 1.5.11 from github via the following command: if (!requireNamespace("devtools", quietly = TRUE)){ install.packages("devtools") } devtools::install_github("kvittingseerup/IsoformSwitchAnalyzeR", build_vignettes = TRUE) ...
written 6 days ago by kristoffer.vittingseerup1.9k
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Comment: C: see reads in .bam file, no counts after HTseq
... The core functionality of HTSeq and featureCounts is identical so I would have to argue there is no need to switch. If you want more accurate quantification you would need to use pseudo-alligners such as Kallisto or Salmon instead. Their main advantages are: 1) they can handle multimappers (featureC ...
written 11 days ago by kristoffer.vittingseerup1.9k
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Comment: C: see reads in .bam file, no counts after HTseq
... Also is it just for 1 gene or is it for all genes you dont get any counts? ...
written 11 days ago by kristoffer.vittingseerup1.9k
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Comment: C: Can I convert from PSI to RPKM?
... How did you originally map/quantify your data (befor running MISO)? Maybe I can suggest a quick way to obtain transcript level quantifications ;-) ...
written 11 days ago by kristoffer.vittingseerup1.9k
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Answer: A: denovo transcriptome assembly
... The best approach is to generate a combined transcriptome from all your samples. You can read more about it, along with some suggestion for bioinformatic tools [here][1]. [1]: https://bioconductor.org/packages/devel/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR.html#what-qu ...
written 13 days ago by kristoffer.vittingseerup1.9k
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Comment: C: Analysis rMATS of RNA Seq data
... I honestly think of the better overviews is a post I wrote here on Biostars recently which introduce the different types of splicing analysis one can do along with mentioning the appropriate tools. You can find it [here][1]. From there you can choose the type of analysis that is of interest to your ...
written 13 days ago by kristoffer.vittingseerup1.9k
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Comment: C: Alternative splicing analysis following kallisto?
... Hi Dina Sorry for not seeing this earlier. Did you solve this problem? ...
written 13 days ago by kristoffer.vittingseerup1.9k
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Answer: A: RNA seq data shows no gene expression but qPCR shows the same gene is upregulate
... In my expression false zero expression of genes happens most commonly if haplotypes are considered whereby multiple (almost) identical version of the genes will be quantified - and since old school (aka on the verge of obsolete) methods only counts uniquely mapped genes there will be zero counts. ...
written 18 days ago by kristoffer.vittingseerup1.9k
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Comment: C: What is the most suitable normalisation technique for RNASeq data?
... +1 from me. An essential step is the inter-library normalization done via the ```normalized=T```. You can read more about why that is needed [here][1]. [1]: https://haroldpimentel.wordpress.com/2014/12/08/in-rna-seq-2-2-between-sample-normalization/ ...
written 18 days ago by kristoffer.vittingseerup1.9k

Latest awards to kristoffer.vittingseerup

Scholar 10 weeks ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Teacher 3 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
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Alternative splicing analysis following kallisto?
Teacher 3 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
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Alternative splicing analysis following kallisto?
Teacher 3 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
Scholar 3 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
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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
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Alternative splicing analysis following kallisto?
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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Scholar 6 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
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Scholar 6 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Teacher 6 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
Scholar 7 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Teacher 7 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
Teacher 7 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
Scholar 8 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
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