Download and run the Python file on Command-Line. Currently, there are four parameters required for input:
- Location of GENCODE File
- Location of FANTOM Metadata file
- Location of FANTOM/Other folder containing experimental data files corresponding to each lncrna
- Location of output csv file
Run the following help command to see description and sequence of inputs (Please input location of Python file on your local system)
python3 /Users/sanatmishra27/Desktop/GOLDLAB.py -h
To run the entire programme with the appropriate arguments (Please input locations of files on your local system)-
python3 /Users/sanatmishra27/Documents/FINAL_GOLDLAB.py -g /Users/sanatmishra27/Downloads/GOLDLab/hum_gencode_v33\ \(1\).txt -meta /Users/sanatmishra27/Downloads/fantom6_metadata.txt -fantom /Users/sanatmishra27/Downloads/FANTOM -o /Users/sanatmishra27/Downloads/GOLDLab/
The filename of each experiment should be the experiment id. For example, ASO_C0008586_03.txt
The folder containing these files needs to be specified as input while running the programme.
The metadata file must have the following columns -
File_Name ENSEMBL CHR strand SYMBOL TSS SPECIES ENTREZID FILE_TYPE PERTURBATION DATASET
Only those genes which satisfy the following criteria are considered for evaluating the test-statistic:
- Genes on the same chromosome as the knocked-down lncrna
where
- n = Number of genes that pass the filters
- d = Distance of gene from UMLILO
- a = Exponent (Set as 1)
The format of the output csv file will be as follows -
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