Combined with the arguments for data loading and normalizing you can use the flags described below for the final half-life calculations.

`-h`

followed by the number of the current calculation for doing several methods at once.
`-h1` |
`method` |
First method for calculation of half-lives (e.g. 'pre' for pre-existing/total based, 'new' for newly transcribed/total based or 'new/pre' for newly transcribed/pre-existing based calculations) |

... | ||

`-hn` |
`method` |
n-th method for half-life calculation |

`-t` |
`time` |
Labeling time point for which calculation will be done |

`-plot` |
`BOOLEAN` |
TRUE if half-life calculations should be plotted. |

`-bias` |
`BOOLEAN` |
TRUE if bias correction should be performed and used before half-life calculation. For this
method to work you have to also use the `-R` , `-ur` and `-ufo` flags. |

`-corr` |
`numerical` |
The half-life median that will be used for median-based correction factor calculation; for '-corr -1' the median will be calculated from your half-life calculations |

`-o` |
`filename` |
Name of the file in which the half-life values will be written |

`-w` |
`printing information` |
Which information will be printed: 'halflife', 'ratio' or 'both' |

`-m` |
`methods` |
The half-life calculation methods whose results should be included in the output;
these methods have to be a subset of the previously defined methods for calculation.
If no list of methods is specified, every calculation will be printed. The methods are
called `pre` , `new` and `new/pre` (see above);
for more than one method please separate the methods with commas (e.g. '-m pre,new') |

`-o`

, `-w`

and
`-m`

combined.```
-i data.txt -ct totalRNA2 -cp preexistingRNA2 -cn newlytranscribed_HumanExon2 -l standard -h1 new -h2 pre -h3 new/pre
-t 60 -o halflives.txt -w halflife -m new,pre,new/pre
```

HALO documentation