User: k.vitting.seerup

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Posts by k.vitting.seerup

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Comment: C: FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
... For trimming I am using [Trimmomatic][1] and it does not specifically matter which filtering you are doing but when you trim paired data the result is 4 files (see "Paired End Mode" section of the [manual][2]) two which contains the ordered paired reads and two files containing respectively the left ...
written 3 months ago by k.vitting.seerup90
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Comment: C: FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
... I think you might have mis-understood me due to me not being clear - sorry about that :-). What I am talking about is not mixing single-end and paire-end libraries. I am talking about the case where a paired end library where trimming of low quality reads etc (via e.g. Trimmomatic) causes the remova ...
written 3 months ago by k.vitting.seerup90
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Comment: C: FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
... Hi Yang Thanks for clarifying this - and yes you are right it contain a mixture of paired and unpaired reads. Why would featureCounts not support mixed paired or unpaired reads? Means that if I have paired end data that needs trimming I will throw away a lot of data - often 5-15%... I think I was ...
written 3 months ago by k.vitting.seerup90
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FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
... **Summary** It seems featureCounts under certain circumstances ignores the ```isPairedEnd = TRUE``` argument. **Background** I have been using featureCounts successfully for many years but recently ran into a problem in files where I have a mixture of paired and unpaired strand specific data (P ...
rsubread featurecounts written 4 months ago by k.vitting.seerup90 • updated 3 months ago by Wei Shi3.1k
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Comment: C: error in aSwitchlist (isoformswitchanalyzeR)
... That is a known problem. UCSC does not have gene_ids which means you cannot directly use the with IsoformSwitchAnalyzeR (since it relies on gene_ids). So you would need to manually "concatenate" transcripts into genes. There are some lists hidden somewhere on UCSC where you can find txid conversion ...
written 4 months ago by k.vitting.seerup90
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Answer: A: error in aSwitchlist (isoformswitchanalyzeR)
... Thanks for clarifying versions above. The problem is that I have hardcoded the min Jaccard similarity of the annotation and the quantification to prevent people from using the wrong annotation with their quantifications. And as you can see the JC similarity is 0.948 (so close). When I recalculate it ...
written 4 months ago by k.vitting.seerup90
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Comment: C: error in aSwitchlist (isoformswitchanalyzeR)
... Could you try updating to 1.5.6 (from the devel branch) and see if the problem persists? You can find the installation instructions [here][1]. Remember to restart your R session after the update. Cheers Kristoffer [1]: https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html ...
written 4 months ago by k.vitting.seerup90
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Comment: C: error in aSwitchlist (isoformswitchanalyzeR)
... Which version of IsoformSwitchAnalyzeR are you using? Cheers Kristoffer ...
written 4 months ago by k.vitting.seerup90
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Comment: C: Parallel computing for IsoformSwitchAnalyzeR
... You are right that DEXSeq is infeasible (it scales exponentially with number of samples) so it would need to be DRIMSeq. Your code looks good. You could try filtering a bit more strict - I would suggest setting IFcutoff=0.1 - meaning you are only considering isoforms which on average contribute with ...
written 5 months ago by k.vitting.seerup90
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Answer: A: Parallel computing for IsoformSwitchAnalyzeR
... Hi Maya Thanks for reaching out. Unfortunately there is no way of doing that from within IsoformSwitchAnalyzeR at the moment. That said the runtime of DRIMSeq mostly scales with the number of transcripts analyzed (and a little bit with the number of samples) so if you just make sure to use preFilte ...
written 5 months ago by k.vitting.seerup90

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