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a-slide / NanoCount

EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
https://a-slide.github.io/NanoCount/
MIT License
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TPM values do not sum up to 1 million #3

Closed lpryszcz closed 4 years ago

lpryszcz commented 4 years ago

Hi, when I ran nanoCompare on my data (dRNAseq mapped with minimap2) I obtained weird TPM values that sum to 5.86092000e+11 6.12210923e+12 3.26647657e+12 1.93848398e+09 instead of 1e6. When I TPM normalise them later on everything seems fine. Any idea?

NanoCount TPM values nanocount scatter

NanoCount TPM values TPM normalised nanocount scatter tmp_norm

NanoCount est_count values TPM normalised nanocount scatter est_count_norm

NanoCount raw values TPM normalised nanocount scatter raw_norm

a-slide commented 4 years ago

Hi @lpryszcz and @tleonardi, I realise that it took me a bit of time to do it, but this is now fixed :s together with a bunch of other problems and optimizations. I will close the issue, but please reopen if you think otherwise Cheers