User: kristoffer.vittingseerup

Reputation:
1,000
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Trusted
Location:
European Union
Twitter:
@kvittingseerup
Last seen:
9 hours ago
Joined:
3 years, 8 months ago
Email:
k***********************@bio.ku.dk

Posts by kristoffer.vittingseerup

<prev • 176 results • page 1 of 18 • next >
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Comment: C: Analysis Without Replicates
... Sounds like a good plan, especially with the log2FC shrinkage - just remember log2FC != pvalues ...
written 13 hours ago by kristoffer.vittingseerup1000
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Answer: A: Could you please tell me how should I analyze the difference between KO and WT m
... I highly recomend Seurat to do the analysis downstream of quantification - it is easy to use, fast, have a very detailed workflows one can follow (fx [this][1]) and most importantly it is one of the best tools for clustering single cell data (according to [this article][2]). With regards to how to ...
written 13 hours ago by kristoffer.vittingseerup1000
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Comment: C: Is Kallisto good for identifying non-coding RNA in a RNAseq data?
... I don't think miRNA should be a problem with standard RNA-seq as the miRNA are typically shorter than fragments analyzed due the size-selection step in the library prepreation. ...
written 3 days ago by kristoffer.vittingseerup1000
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Comment: C: Is Kallisto good for identifying non-coding RNA in a RNAseq data?
... True Kallisto is better suited for long-noncoding RNAs (lncRNAs) ...
written 4 days ago by kristoffer.vittingseerup1000
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Answer: A: Is Kallisto good for identifying non-coding RNA in a RNAseq data?
... Yes. Kallisto does not distinguish between coding and non-coding. It only requires that the transcripts are already annotated (so if you are looking for novel lncRNAs you should use a different pipeline). What is the frequency of lncRNAs in the transcript annotation database to start with? ...
written 5 days ago by kristoffer.vittingseerup1000
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Comment: C: How to deal with the case that one gene symbol matches multiple ensembl ids?
... Yes just use gene_ids (such as Ensemble ids). Using that you get an expression matrix just like normal (except slightly larger) which you can do all downstream analysis with. Which "name" you assign to a gene (gene name, symbol or id) does not matter for the downstream analysis. With regards to why ...
written 5 days ago by kristoffer.vittingseerup1000
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Comment: C: How to identify RNA-seq mapped reads to reference genome but not identified by f
... The simplest way is to define introns as the regions between exon and the intergenic regions as those between genes. If you are actually looking for code to do this you should make a new question. ...
written 6 days ago by kristoffer.vittingseerup1000
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Comment: C: Why is my features different between featurecounts and cuffnorm?
... If that is the case I strongly reccomend using Salmon or Kallisto. Kallisto can be downloaded from [here][1] and the manual for running Kallisto can be found [here][2]. Salmon can be downloaded from [here][3] and a manual for running Salmon can be found [here][4]. I actually wrote a entire section a ...
written 6 days ago by kristoffer.vittingseerup1000
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Comment: C: Statistical comparison of expression of two _different_ genes
... Does such a thing exists? ...
written 6 days ago by kristoffer.vittingseerup1000
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Statistical comparison of expression of two _different_ genes
... I am interested in a comparing expression of gene_A vs gene_B in a homogenous population. If you don't have the number of samples to do a non-parametric test how would one do a parametric statistical comparison? My thoughts are as follows: 1. Gene length normalisation is essential. TPM (transcrip ...

Latest awards to kristoffer.vittingseerup

Scholar 5 days ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Teacher 7 days 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 26 days ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Teacher 26 days 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 4 weeks 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 weeks ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Teacher 8 weeks 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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Supporter 10 weeks ago, voted at least 25 times.
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 14 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Scholar 15 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Scholar 17 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Teacher 17 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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