Moderator: igor
igor ♦ 6.5k
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Posts by igor
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... Additionally, if you know how you will be analyzing the data, you may want to check the instructions for that pipeline. Many single-cell analysis packages now include a function to read 10x matrix and convert it to the most appropriate format for that package. ...
written 7 hours ago by
igor ♦ 6.5k
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... And how are you generating these bedGraphs? ...
written 2 days ago by
igor ♦ 6.5k
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... You should check a known housekeeping gene like ACTB or GAPDH before you check some obscure transcript that may not be real. ...
written 3 days ago by
igor ♦ 6.5k
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... Additionally, if you say "hg19" or "hg38", that is actually not entirely accurate either. This post illustrates that problem very clearly: http://lh3.github.io/2017/11/13/which-human-reference-genome-to-use
Unless you are embedding the entire reference FASTA, you really can't be entirely sure what ...
written 7 days ago by
igor ♦ 6.5k
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... Non-robust should be the classic FPKMs. If you check the column sums (`colSums`), they should all add to 1M then. ...
written 8 days ago by
igor ♦ 6.5k
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... Yes. But if the samples are processed separately, you will likely have batch differences. That's a much more complex issue. ...
written 8 days ago by
igor ♦ 6.5k
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131
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... By default, DESeq2's `fpkm()` will return "robust" FPKMs, which use size factors to normalize instead of taking the column sums of the raw counts. ...
written 9 days ago by
igor ♦ 6.5k
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... Thank you. That was very helpful.
...
written 13 days ago by
igor ♦ 6.5k
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Comment:
C: Seurat -FindVariableGenes problem
... Yes. Follow the instructions in the tutorial. There are a lot of steps and they have a specific order. ...
written 15 days ago by
igor ♦ 6.5k
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89
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Comment:
C: Seurat -FindVariableGenes problem
... This may or may not be causing the error, but `x.low.cutoff` (bottom cutoff on x-axis for identifying variable genes) should probably be higher than 0. ...
written 16 days ago by
igor ♦ 6.5k
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For Why are there multiple GFP nucleotide sequences?
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