PIT
- Requirements
- python3
- docker
install docker image with
docker pull nirkoty/pit
Running PIT requires writting a configuration file that contains the paths to the input files, defines the conditions and samples in the experiment and mass spectrometry runs. Below is a template of how to write the config file. Examples are provided in the "examples" folder.
{
"output": "PATH TO OUTPUT FOLDER",
"reference_fasta": "PATH TO REFERENCE GENOME FASTA FILE FOR REFERENCE GUIDED ASSEMBLY",
"reference_gff": "PATH TO REFERENCE GENOME ANNOTATION (GTF) FILE FOR REFERENCE GUIDED ASSEMBLY",
"threads": 12,
"ms":{
"runs": {
"RUN_NAME":{
"files": [PATHS TO RAW FILES],
"modifications": {
"fixed": [
USE MAXQUANT NOTATION FOR PTM
],
"variable": [
]
},
"TMT": {
"Nsi/1": "126",
"Nsi/2": "127C",
"Nsi/3": "128C",
"Nsi/4": "129C",
"si/1": "127N",
"si/2": "128N",
"si/3": "129N",
"si/4": "130N",
}
}
}
},
"mutations": true,
"splicing": true
"conditions": {
"CONDITION NAME": {
"SAMPLE NAME":{
"left": "PATH TO FASTQ FORWARD FILE",
"right": "PATH TO FASTQ REVERSE FILE"
}
}
}
}
The analysis can be started with docker using the command
python3 LaunchDocker.py -c PATH_TO_CONFIG_FILE -r
or with singularity using the command
python3 LaunchDocker.py -c PATH_TO_CONFIG_FILE -r -s PATH_TO_SINGULARITY_IMAGE