Transit Gumbel - Gene ID does not match

I am using Transit Gumbel tool to determine gene essentiality from my transposon libraries using the tutorial titled “Essential genes detection with Transposon Insertion sequencing”.

However, the Gene ID (“orf” column) that was generated does not exactly match the gene ID of my organism. The gene ID generated was listed as multiples of 5 (D7S_RS00010, D7S_RS00015, D7S_RS00020, etc).

  1. Any ideas on what have gone wrong?
  2. I suspected that maybe I uploaded the wrong “type” of file from NCBI, instead of the gene annotation file. How do you upload gene annotation file (in the gff3 format) from NCBI to your history?

Thank you all!

Capture the link from the genome page at NCBI and paste that URL into the Upload tool in Galaxy. Use all default settings.

Here is an example of where to find the file for a human build:

Thank you for the advice!

1 Like