About the read density in the output file

smithlabcode / ribotricer

A tool for accurately detecting actively translating ORFs from Ribo-seq data

http://doi.org/djv4

GNU General Public License v3.0

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About the read density in the output file #148

Closed lbwfff closed 6 months ago

lbwfff commented 6 months ago

Hi, saketkc

I would like to confirm the definition of the 'reads density' column in the final output file of Ribotricer. Are the 'reads' here not normalized, similar to ‘Counts’ in RNA-seq?

Thanks, LeeLee

saketkc commented 6 months ago

The read density is simply: (number of uniquely mapped reads)/(orf length). I would recommend using DESeq2 or related tools for normalization of the counts matrix.