run_preCluster.py

[jordur]

Hi!
I would like to analyze some PacBio data without a reference genome. To this end, I tried to follow the following tutorial:
https://github.com/Magdoll/cDNA_Cupcake/wiki/Tutorial:-Collapse-redundant-isoforms-without-genome
I used cd-hit but then I was unable to find the run_preCluster.py script.
I saw here that it was a piece of software from cDNA_cupcake. However, after being installed, I did not find the script neither in the git repository nor in the build directory created after running python setup.py build.
I just found a reference about the run_preCluster.py on the README.md page:
2019.12.30 updated to v9.2.0. fixed support for running run_preCluster.py that is used by Cogent

Since I would like to run the family finding over a large dataset (~ 91857 sequences), can anyone give me a clue about how to analyze such a large dataset?
Regards,

[Magdoll]

Hi @jordur - preCluster.py is no longer supported. Most of the Cupcake code is on its way to getting deprecated.
If you have Iso-Seq data, I recommend going to isoseq.how for the latest software.

-Liz