User: elle

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elle10
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Germany
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4 years, 4 months ago
Joined:
4 years, 6 months ago
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Posts by elle

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Answer: A: Incongruencies between DEXSeq and BitSeq/Cuffdiff
... I'm sorry, I can't really provide the transcript and gene IDs as it's from an ongoing study and I'm not allowed to public these information. Really thank you for the explanations, it was of great help :)   ...
written 4.4 years ago by elle10
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Comment: C: Incongruencies between DEXSeq and BitSeq/Cuffdiff
... And sorry if I didn't add other information about the previous example but I thought it would be more meaningfull to discuss the updated results. ...
written 4.4 years ago by elle10
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Answer: A: Incongruencies between DEXSeq and BitSeq/Cuffdiff
... Hi! Sorry for the late reply. I'll post here another example with the analysis made with DEXSeq 1.14. For this gene DEXSeq report a differential usage of exon/bin E005 with a log2FC of -0.52. The Transcript ID related to this exon/bin in DEXSeq results to be significantly differentially expressed i ...
written 4.4 years ago by elle10
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Comment: C: Incongruencies between DEXSeq and BitSeq/Cuffdiff
... This plot refers to the exons expression. I'd say that exons 001 and 003 are not significantly differentially expressed because other isoforms which contain them are expressed in such a way that the overall count for these exons is the same in the 2 conditions. My concern in the plot is about exon 2 ...
written 4.5 years ago by elle10
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Comment: C: Incongruencies between DEXSeq and BitSeq/Cuffdiff
... I was also discussing with others about the possible biological explanation for the observed discepancies. Would it be possible that even if some of the isoforms containing one exon are more expressed or constant between 2 conditions the specific exon results less expressed, maybe because taking int ...
written 4.5 years ago by elle10
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Answer: A: Incongruencies between DEXSeq and BitSeq/Cuffdiff
... Thanks! I'll try with the example you suggested. Here there is one exampe of plot that I found confusing, as the counts for the exon 002 seem to be quite different between the 2 conditions, while the log2fc for the same exon was only 0.22 ...
written 4.5 years ago by elle10
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Answer: A: Incongruencies between DEXSeq and BitSeq/Cuffdiff
... Thanks for your replies Steve and Alejandro. To be honest is not totally clear to me how the plotDEXSeq function would help me to understand why an isoform has not been called differentially expressed. On the contrary, even without  comparing to the BitSeq/Cuffdiff output I found these plot a bit co ...
written 4.5 years ago by elle10
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Incongruencies between DEXSeq and BitSeq/Cuffdiff
... Hi! I am studying alternative splicing in some genes. The original data were analyzed a couple of years ago with DEXSeq (I ignore which version was used as the analysis was done by a previous colleague). To integrate the information about exon usage with infomration about differential isoform expre ...
dexseq bitseq isoforms cuffdiff differential exon usage written 4.5 years ago by elle10
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Answer: A: using BitSeq data as input for spliceR
... Thank you very much!   ...
written 4.5 years ago by elle10
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Answer: A: using BitSeq data as input for spliceR
... I have other questions. The command for getGeneExpression requires the trInfoFile and a file like "data-GE.rpkm". The trInfoFile are produced during the parseAlignment step (the very first step), I imagine that if I run the basic pipeline I won't be able to retrieve these files in the future, so if ...
written 4.5 years ago by elle10

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Popular Question 4.4 years ago, created a question with more than 1,000 views. For Incongruencies between DEXSeq and BitSeq/Cuffdiff

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