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GoekeLab / xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing
https://xpore.readthedocs.io/
MIT License
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output of diffmod and xpore post processing #168

Closed rezarahman12 closed 1 year ago

rezarahman12 commented 1 year ago

Dear xPore team,

The output of xPore and xpore post-prcoessing table does not have chromosome column.

I have given the screenshot of my output file. Could you please tell me why the chromosome file is missing?

image Thank you for your time and help. Best regards Reza

yuukiiwa commented 1 year ago

Hi Reza (@rezarahman12),

The current version of xPore doesn't output a chromosome column. We can implement that for the next release.

Thanks!

Best wishes, Yuk Kei

rezarahman12 commented 1 year ago

Thanks, Yuk Kei for letting us know. Yes, that will be an excellent option if you kindly add that feature.

For now, could you please help me get the chromosomes of those genes identified? Kind regards Reza

yuukiiwa commented 1 year ago

Hi Reza (@rezarahman12),

I have implemented a function to include the chromosome and gene id through xpore postprocessing in the add_chr_gname branch, you can try running this with the following:

  1. download xpore-add_chr_gname branch: https://github.com/GoekeLab/xpore/archive/refs/heads/add_chr_gname.zip
  2. after unzipping the folder then go into the folder with cd xpore-add_chr_gname and install xpore with the following (add sudo if necessary): 
    python3 setup.py install
  3. Ran xpore postprocessing with the following: 
    xpore postprocessing --diffmod_dir [diffmod output directory] --gtf_or_gff [gtf file used in dataprep] --genome

Thanks!

Best wishes, Yuk Kei

rezarahman12 commented 1 year ago

Hi Yuk Kei (@yuukiiwa ) Thank you so much for your big help. It worked well. Many thanks Reza