filter-out option no work for SE reads

[y9c]

No description provided.

[timedreamer]

Hi, I'm facing this problem also. Any solutions so far?
I got the error UnboundLocalError: local variable 'read1' referenced before assignment

Thanks!
Ji

[IanSudbery]

Hi, I just merged the PR from @yech1990 that should fix this. If you are able to install the latest from master, it should work. Let me know if you need help with that.

[timedreamer]

Hey great! If you could help with installing from master, that would be great! I used conda to install before. I can wait for the conda version too, if it doesn't take long. Thanks!

[IanSudbery]

Hi @timedreamer

I don't know how long the conda release will be as @TomSmithCGAT normally rolls these once there are a few changes to bundle up.

To install from master:

1. Activate your conda environment.
2. Download/clone the code to any location of your choice with:
   git clone https://github.com/CGATOxford/UMI-tools.git
3. Enter the UMI-tools directory:
   cd UMI-tools
4. Install:
   python setup.py install

You can delete the downloaded/cloned directory if you wish at this point.