What does the (norm) suffix mean in the miRDeep2 quantifier.pl output file?
Hello everyone!
I've run the miRDeep2 quantifier.pl pipeline on 12 samples, and have gotten a nice results table. However, it looks like this:
miRNA read_count precursor total s01 s02 s01(norm) s02(norm)
hsa-let-7a-5p 60215100 hsa-let-7a-1 60215100 3933700 2594200 5499125 835850
So I'm wondering what the s01(norm) and s02(norm) is? Normalized numbers? And if so, how are these normalized and with regards to what?
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Nicolai Skovbjerg Arildsen •
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Nicolai Skovbjerg Arildsen •
1 answer
yes,the suffix means normalization, the code indicates it is a tpm:
## Author: SM
## Date: 04/04/2019
## read normalization is now 1e6 * mature-reads/all_mature_reads (So reads per million mapped miRNA reads)
## precursors with 0 read mappings cryptic warning messages to stderr removed
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