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Question: What does the (norm) suffix mean in the miRDeep2 quantifier.pl output file?
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gravatar for Nicolai Skovbjerg Arildsen
5 months ago by
Nicolai Skovbjerg Arildsen • 0
Sweden
Nicolai Skovbjerg Arildsen • 0 wrote:

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?
mirna rna-seq mirdeep2 • 210 views
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modified 5 months ago by JC ♦ 12k • written 5 months ago by Nicolai Skovbjerg Arildsen • 0
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gravatar for JC
5 months ago by
JC ♦ 12k
Mexico
JC ♦ 12k wrote:

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
ADD COMMENT • link written 5 months ago by JC ♦ 12k
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