User: kristoffer.vittingseerup
kristoffer.vittingseerup • 3.4k
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- @kvittingseerup
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Posts by kristoffer.vittingseerup
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... Did you run StringTie --merge as well? You can read more about the workflow [here][1].
And yes if you have a suspicion you migh have novel transcripts I recommend running StringTie.
[1]: https://bioconductor.org/packages/devel/bioc/vignettes/IsoformSwitchAnalyzeR/inst/doc/IsoformSwitchAnalyzeR. ...
written 2 days ago by
kristoffer.vittingseerup • 3.4k
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... IsoformSwitchAnalyzeR can work directly from the "rsem.isoforms.results". I suggest you take a look at the [quick start][1] part of the vignette which should describe exactly what you need including code you can use.
[1]: https://bioconductor.org/packages/devel/bioc/vignettes/IsoformSwitchAnalyz ...
written 5 weeks ago by
kristoffer.vittingseerup • 3.4k
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... I would as you suggest use `vst` and then afterwards normalize for gene-length as well ( `vst / gene_length * 1e3` ). You could check with the [cqn package][1] if GC normalisation seems to be needed.
[1]: https://www.bioconductor.org/packages/release/bioc/html/cqn.html ...
written 6 weeks ago by
kristoffer.vittingseerup • 3.4k
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... Could you clarify if you did any transcript assembly with StringTie? Also how did you take into account the paired nature of your samples in your DE analysis? Could you post a genome browser screenshot of the HOX4 gene problem? ...
written 9 weeks ago by
kristoffer.vittingseerup • 3.4k
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... I'm not an expert in Ribo-seq but I don't think you can directly use an RNASeq pipeline as there are many QC steps you want to consider when handling Ribo-seq data (codon frequency etc). Have you looked at some ribo-seq pipelines? ...
written 9 weeks ago by
kristoffer.vittingseerup • 3.4k
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... You should get your collegues to give you the count data. Whichever tool calculated the TPM values most likely also calculated the (estimated) counts. Also please note if you don't have the raw data you cannot publish as that is a requirement for reproducibility. ...
written 9 weeks ago by
kristoffer.vittingseerup • 3.4k
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... That does indeed look very stange! How did you quantify your samples? How many samples do you have? Did you do any filtering before using voom - if so how? ...
written 10 weeks ago by
kristoffer.vittingseerup • 3.4k
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... I would just use the save() or saveRDS() function to save the R object(s), transfer them and then use load() or readRDS() to open them on your local computer. ...
written 10 weeks ago by
kristoffer.vittingseerup • 3.4k
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... I'm not sure. Somehow the --merge option does not consider this a propper transcript (which I might also doubt as it is >1000 nt without any introns and does not appear to be identical in any samples?). Did you try running stringtie --merge with the "-i" option? ...
written 10 weeks ago by
kristoffer.vittingseerup • 3.4k
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... Kallisto sounds like a good approach. With regards to IsoformSwitchAnalyzeR It is not appropriate to ask a new question as a comment (since it makes it very hard for other people to find/navigate the info/solutions). Either ask it as a new question here on biostars or in the IsoformSwitchAnalyzeR [g ...
written 10 weeks ago by
kristoffer.vittingseerup • 3.4k
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