Moderator: igor
igor ♦ 12k
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... I don't know if it's strange. Even model organisms are manually annotated (many tools exist, but they are usually not sufficient for publication-level analysis). It would be harder to do this for non-model organisms. ...
written 10 days ago by
igor ♦ 12k
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Comment:
C: TMM normalized TPM
... No. But you can convert FPKMs to TPMs with a simple formula. See: https://www.biostars.org/p/273370/ ...
written 10 days ago by
igor ♦ 12k
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... Do you mean something more advanced than just using a closely related organism? ...
written 10 days ago by
igor ♦ 12k
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... Doesn't Fluidigm C1 have a UMI option? ...
written 11 days ago by
igor ♦ 12k
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... Most under-appreciated benefit: I can take a perl script from 10 years ago and it will work 95% of the time. Which other mainstream bioinformatic language can you say that about? ...
written 18 days ago by
igor ♦ 12k
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Comment:
C: Annotate PBMC scRNA-seq data
... There are multiple discussions on this site about scRNA-seq cell annotation. ...
written 19 days ago by
igor ♦ 12k
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... In case of 3' datasets, theoretically one transcript results in one count regardless of length, so TPM would be the same as CPM. You would not need to perform additional gene length normalization.
Caveat: if you want to account for technical variables like internal priming, things get more complica ...
written 4 weeks ago by
igor ♦ 12k
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... It's unfortunate that the main output of the paper is not more clearly described.
Curiously, not all of those 613 genes are present in the "OneSubtypeVStheRest" tables. ...
written 4 weeks ago by
igor ♦ 12k
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... That sounds reasonable. but what do `sam`, `9`, and `8` refer to? ...
written 4 weeks ago by
igor ♦ 12k
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Answer:
A: Annotate PBMC scRNA-seq data
... You can check this tutorial for working with a scATAC and scRNA-seq dataset where they also use PBMC data: https://satijalab.org/signac/articles/pbmc_vignette.html ...
written 4 weeks ago by
igor ♦ 12k
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