Improved T cell Receptor Antigen Pairingthrough data-driven filtering of sequencing information from single-cells
This repository contains the code to identify ITRAP filters for single-cell immune profiling data.
ITRAP is developed by Morten Nielsen's group at the Technical University of Denmark (DTU). ITRAP code and data can be used freely by academic groups for non-commercial purposes. If you plan to use ITRAP or any data provided with the script in any for-profit application, you are required to obtain a separate license (contact Morten Nielsen, morni@dtu.dk).
For scientific questions, please contact Morten Nielsen (mniel@dtu.dk).
Designed with snakemake workflow (v5.7.4)
snakemake --config exp=exp13 run=run1 --use-conda
Each script may also be run by command line. For help run scripts/ -h The Snakefile links the required environments for each script. The environment files are found in envs/.
Anaconda or other Python source (Python 3.7.3) Specific requirements for each script are logged in envs/
The pipeline expects a TSV file indexed by 10x barcodes, i.e. GEMs, containing features of TCR, pMHC, & cell hashing. These features may be generated using Cellranger multi.
The pipeline expects database of TCR-pMHC annotated sequences, which is stored in tools/tcr_dbs.csv.gz.