User: kristoffer.vittingseerup
kristoffer.vittingseerup • 2.4k
- Reputation:
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- Twitter:
- @kvittingseerup
- Last seen:
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- Joined:
- 4 years, 7 months ago
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Posts by kristoffer.vittingseerup
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... 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.vittingseerup • 2.4k
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... 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.vittingseerup • 2.4k
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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.vittingseerup • 2.4k
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... 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.vittingseerup • 2.4k
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... 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.vittingseerup • 2.4k
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... Why would you want analyse the distribution in each file? To look for differences between groups? ...
written 11 days ago by
kristoffer.vittingseerup • 2.4k
1
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1
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... 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.vittingseerup • 2.4k
0
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1
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137
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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.vittingseerup • 2.4k
1
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1
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213
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... 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.vittingseerup • 2.4k
2
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1
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186
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... 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.vittingseerup • 2.4k
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