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Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.

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vanallenlab/retained-intron-neoantigen-pipeline

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retained-intron-neoantigen-pipeline

This pipeline calls RNA-based neoantigens from intron retention events derived from RNA-Seq data and identified through the KMA package (see run instructions below for further detail on this).

To run:

  • Download NetMHCPan-3.0 (http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCpan) and change paths in runNetMHCpan.py file (line 62).
  • Download twoBitToFa utility from UCSC genome browser (https://genome.ucsc.edu/goldenpath/help/twoBit.html) and change paths in kmaToPeptideSeqs.py file (line 173).
  • Download MySQL (you will use it to query the UCSC table browser via public servers).
  • Download and run KMA-kallisto package (https://github.com/pachterlab/kma/blob/master/inst/kma-kallisto.zip). The output from this package (ir$flat file, example files run_kma_example.R and kma_output_file_example.csv in this repo) will be the direct input to this pipeline.
  • Change paths in shell script getNeoantigenBinders.sh (notes in file comments).
  • Run getNeoantigenBinders.sh from command line as an SGE Array Job. This script is a wrapper and will call all other relevant Python scripts.

Additional notes:

  • Detailed execution instructions and functionality descriptions can be found in each script header, as well as for each individual function.
  • Feel free to create an Issue if errors arise.

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Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.

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