User: kristoffer.vittingseerup
kristoffer.vittingseerup • 1000
- Reputation:
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- European Union
- Twitter:
- @kvittingseerup
- Last seen:
- 9 hours ago
- Joined:
- 3 years, 8 months ago
- Email:
- k***********************@bio.ku.dk
Posts by kristoffer.vittingseerup
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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.vittingseerup • 1000
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... 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.vittingseerup • 1000
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... 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.vittingseerup • 1000
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... True Kallisto is better suited for long-noncoding RNAs (lncRNAs) ...
written 4 days ago by
kristoffer.vittingseerup • 1000
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... 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.vittingseerup • 1000
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... 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.vittingseerup • 1000
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... 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.vittingseerup • 1000
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... 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.vittingseerup • 1000
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... Does such a thing exists? ...
written 6 days ago by
kristoffer.vittingseerup • 1000
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... 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 ...
written 7 days ago by
kristoffer.vittingseerup • 1000
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For A: How to deal with the case that one gene symbol matches multiple ensembl ids?
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For A: RNA-seq analysis between 2 closely related strains of the same species
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For A: RNA-seq analysis between 2 closely related strains of the same species
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