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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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Normalised the reads count #33

Closed M-Chi-1 closed 6 months ago

M-Chi-1 commented 8 months ago

Hi,

I would like to quantify the gene expression in treated and untreated condition. The total reads count is low in my treated condition. So I am wondering would the nanocount take in consideration the difference in the total reads count or do I need to down samples the total reads count in both conditions? Please see the attached

Screenshot 2023-11-20 at 13 54 10

Thanks in advance

josiegleeson commented 6 months ago

Hi, keep in mind NanoCount is for transcript expression not gene expression. However, you can still quantify the transcripts in your samples. The output contains a column called 'tpm' which is normalised (transcripts per million) but if you're hoping to run a differential expression analysis, please use the 'est_count' column for the counts as most differential expression programs do their own normalisation for depth. Hope this helps.