kallisto2nanosim

Converting transcript abundance files from Kallisto for NanoSim.
Why is this conversion required?

1. NanoSim can only read TSV-files with exactly three columns but Kallisto outputs five
2. NanoSim has/had a bug where underscores in the target_id will cause it to fail

Examplary usecase:
For the evaluation of hybrid tools using short and long RNAseq reads you might want to simulate long reads with NanoSim that match the expression profile in your short read data.

usage: kallisto2nanosim [-h] [--remove_underscore] kallisto_file nanosim_file

Converting Kallisto transcript abundance files for NanoSim.

positional arguments:
  kallisto_file
  nanosim_file

options:
  -h, --help           show this help message and exit
  --remove_underscore