User: kristoffer.vittingseerup

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European Union
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@kvittingseerup
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Posts by kristoffer.vittingseerup

<prev • 385 results • page 1 of 39 • next >
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Answer: A: Run ASTALAVISTA for large number of files
... I cannot answer the question about ASTALAVISTA - but I will try to answer the question about comparing alternative splicing from the geographically spread accessions (which I interprete as grouped data) via other tools as I think that might be a better solution for your problem. The reason I would ...
written 6 days ago by kristoffer.vittingseerup2.4k
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Comment: C: How splice-aware aligner (RNA-Seq) deal with long gap (intron) penalty
... How a tool solves this problem is specific to the aligner and would most likely be described in the documentation of the aligner of interest - have you tried looking there? ...
written 6 days ago by kristoffer.vittingseerup2.4k
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Comment: C: edgeR gives no DE genes <0.05 FDR
... In addition to the PCA plot of your sample could you post the p-value (not FDR) histogram? Will help us till if the model you build is okay. ...
written 7 days ago by kristoffer.vittingseerup2.4k
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Answer: A: how to change gtf to fasta file of cufflink, gffread
... For most genes you have quantified multiple transcripts. The expression of those transcripts have then been summed to get the gene expression - which is then used to o the gene differential expression. This also means that there is no single sequence which will represent the gene you have been analy ...
written 11 days ago by kristoffer.vittingseerup2.4k
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Answer: A: Transcript vs. Gene TPM counts?
... 1) Gene expression is obtained by summing the expression of all transcripts belonging to the same gene. 2) Yes TPM are normalised values - but you might still need to perform a inter-library normalization. You can read more about that [here][1]. [1]: https://haroldpimentel.wordpress.com/2014/12/ ...
written 11 days ago by kristoffer.vittingseerup2.4k
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Comment: C: Run ASTALAVISTA for large number of files
... Why would you want analyse the distribution in each file? To look for differences between groups? ...
written 11 days ago by kristoffer.vittingseerup2.4k
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Comment: C: Stringie output doesn't have any gene names!
... 1. Look for cases where the StringTie gene is associted with multiple refrence gene names. 2. It's a bit inconvinent for sure - but also a really hard problem. I would rather a tool does not solve a problem unless it does it in a good way. Most people probably use the StringTie IDs to summarize, a ...
written 13 days ago by kristoffer.vittingseerup2.4k
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Comment: C: GSEA for paired RNA-Seq data
... 1. If you just use camera() it will autmatically use the camera.DGElist() if you supply a DGElist. 2: Just use camera on the lrt object in step 4.1.9. ...
written 13 days ago by kristoffer.vittingseerup2.4k
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Answer: A: STAR: Is it ok to align with an index created from genecode but count features f
... You will most likely have a problem. Gencode uses chromosome names: "chr 1", "chr 2" etc. Ensembl uses chromosome names "1", "2" etc. Why not use gencode gtf file? ...
written 18 days ago by kristoffer.vittingseerup2.4k
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Answer: A: Stringie output doesn't have any gene names!
... The problem is that assigning gene names is not trivial since for a subset of the data the genes identified by StringTie (defined as overlapping (re-constructed) transcripts) might overlap multiple genes - then how do you decide which gene name to assign to a specific transcript? This is a very hard ...
written 19 days ago by kristoffer.vittingseerup2.4k

Latest awards to kristoffer.vittingseerup

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 13 days ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Scholar 13 days ago, created an answer that has been accepted. For A: Error while loading the data structrure in the ballgown tool
Scholar 7 weeks ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Teacher 7 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
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Student 7 weeks ago, asked a question with at least 3 up-votes. For Equivavalent of rlog() or vst() for abundance values
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 10 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 3 months 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
Scholar 3 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
Scholar 6 months ago, created an answer that has been accepted. For A: which option is better for DESeq2 analysis: salmon or htseq-count?
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: Alternative splicing analysis following kallisto?
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: Alternative splicing analysis following kallisto?
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 7 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Scholar 8 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Teacher 8 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 8 months ago, created an answer with at least 3 up-votes. For A: Alternative splicing analysis following kallisto?
Scholar 9 months ago, created an answer that has been accepted. For A: download CNV file for breast cancer BRCA from TCGA website
Teacher 9 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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