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rajewsky-lab / mirdeep2

Discovering known and novel miRNAs from small RNA sequencing data
GNU General Public License v3.0
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Set up issue templates #69

Open mschilli87 opened 4 years ago

mschilli87 commented 4 years ago

We should have templates to avoid asking the same questions over and over again and allowing us to simply flag invalid requests as such and close them without wasting our time.

Drmirdeep commented 4 years ago

If people would just read the paper in which the method is clearly described and have a look at the tutorial files then this would not be necessary. I would not waste time on it. It is a minimum requirement for everything to read the tutorial and the manual/described methods in the paper.

Furthermore, if you download files from miRBase and manage to extract hairpins from the downloaded files which are 60 nt long then this is clearly a user input error.

  1. miRNA biogenesis hasn't been understood apparently otherwise 60nt long precursors would not have been extracted
  2. programming skills are not sufficient otherwise 60nt long precursors would not have been extracted
  3. the miRDeep2 included script for doing this properly wasn't used otherwise 60nt long precursors would not have been extracted

It should also be alarming if 1,400 human precursors have the exact same length...

And for every computational tool the GIGO phrase 'Garbage In, Garbage Out' is key for proper results. miRDeep2 is no exception here although over the years we caught many of these faulty usage cases already.