Mutanome & Transcriptome-Derived Neoepitope Discovery System
The following
In order to run NeoStream, the following libraries will also need to be installed:
- cruzdb (https://github.com/brentp/cruzdb)
- HTSeq (https://htseq.readthedocs.io/en/release_0.10.0/)
- Tabix (https://pypi.org/project/pytabix/)
- requests
- pandas
- numpy
- scipy
To begin using NeoStream, clone this Github repository to your computer.
git clone https://github.com/nityxlabs/NeoStream.git
The directory structure should be as follows:
/Algorithm
/Data - contains file for neoepitope comparison 180106_Proteasome_TAP_Chart.txt
/Genome - contains hg19.fa & hg19.fa.fai (samtools-indexed) genome build file
/Results
The hg19.fa build and hg19.fa.fai (samtools-indexed) files should be located in the /Genome directory. To create the samtools
Next, run the following script to set up local genomic databases.
python setup_cruzdb_databases.py
To execute NeoStream, perform the following procedure:
# python script "180820_Pipeline_NeoStream_V2.py [filename] [prefix_label]"
# filename = the file in the ../Data path that is being analyzed (example: PDAC.final.somatic.maf)
# prefix_label = string that will be appended to each output file in the /Results directory (example: 180901)
python 180820_Pipeline_NeoStream_V2.py file.maf 180901The algorithm will output information into the /Results directory:
* [prefix_label]_Thres0_[filename]_ProcessGenomeAlt_V1.txt - generates a list of potential neoepitopes from a given mutation
* [prefix_label]_Thres0_[filename]_NeoepCompare_V1.txt - contains the processing efficiency & MHC affinity for each neoepitope derived from a given mutation
* [prefix_label]_Thres0_[filename]_NeoepCompare_V1_Extended.txt - further identifies information associated with neoepitopes, including assignment of high MHC affinity allele
NOTE: note to self - finish documentation looking at following link: https://gist.github.com/PurpleBooth/109311bb0361f32d87a2