Real numbers in small RNA seq count output using mirdeep2 quantifier.pl.

Question

[13530213]

Hi everyone,

Yesterday/overnight I ran some small-ran-seq alignment using mirdeep2 quantifier.pl). I do have output, however I have some questions that the documentation does not address. So.. I would like to ask you guys instead. So my output looks something like this:

#miRNA  read_count  precursor   total   S01 S02 S01(norm)    S04(norm)
hsa-let-7a-5p   251.98  hsa-let-7a-1    251.98  14.39   11.56   2.99        1.52
hsa-let-7a-3p   9.39    hsa-let-7a-1    9.39    0.02    0.50    0.15        0.03
hsa-let-7a-5p   241.38  hsa-let-7a-2    241.38  14.39   11.56   2.99        1.52
hsa-let-7a-2-3p 2.66    hsa-let-7a-2    2.66    0.01    0.14    0.15        0.04
hsa-let-7a-5p   252.56  hsa-let-7a-3    252.56  14.39   11.56   2.00        1.52
hsa-let-7a-3p   9.37    hsa-let-7a-3    9.37    0.02    0.50    0.15        0.03

1. Most important question: if the S01 and S02 are supposed to be counts, then why are there fractions? Also what is the actual definition of these numbers if they are fractions?
2. How are the (norm) columns normalised?
3. How are read_count and total columns calculated? Is it just the total over all other columns (so, S01 and S02)?
4. How did you figure this out? (just so that I get this skill too.)

Thanks in advance!

[ATpoint]

The Github repository has documentation and a FAQ section: https://github.com/rajewsky-lab/mirdeep2

[13530213]

Thank you @ATpoint. I totally missed the FAQ file. So Q2 in the FAQ answers my second question, or does it also address my first? I am unsure...