CAI[N] Files

Author:André Marqaurdt

Please note: This tool is for research use only!! This tool is NOT for diagnostic purposes!

Dependencies:
Python 2.7 (www.python.org)
SciPy (van der Walt et al., 2011)
Numpy (van der Walt et al., 2011)
Matplotlib (Hunter, 2007)
bowtie2 (Langmead et al., 2009)
fpdf (https://pyfpdf.readthedocs.io/en/latest/)

After downloading the folder "CAIN_release_1_01" you have to adjust some specific paths in order to run the program:
1. Change the default results folder used in the pipline (line 16 in "main.py")
2. Change the "metafile"-path used to the location on your system (line 23). You can find this file in  "CAIN_release_1_01.zip/CAIN_release/data_cain/metafile/"
3. Change all paths used in the "metafile" to the correct paths based on the location on your system.

Running the program:
In order to now run the program you need to start the command line:
direct into the folder where you unpacked the tool.
Then you start the tool with the following command:

python main.py -g [male/female] -p [path to the patient specific fastq.gz file] [-o [path] (if you want to on the fly change the output folder]


Interpreting results:
karyotype_numerical: The usually (gold standard) used karyotype annotation for numerical aberrations
all_random_healthy_counts: Raw Data used for plotting
chromosomal_region_over_under: Different files using either 3 or 2 (stated in the filename) Standard Deviations for decision making, showing all over- or underrepresented Regions without any filtering for biological meaningfulness or length of the gained/lost region. "With proteins" file sadditionally contain information about all genes located in this lost/gained area.
region_plots: Graphical output for all chromosomes, showing the in-silico reference and the considered sample