Acronyms and User Guidelines

This page introduces users with the terminologies related to our workflow and also provides with a guideline to smooth processing of their data through a User guidelines section.

Acronyms and Definitions

  • DL - Deep Learning
  • WES - Whole Exome Sequencing
  • WGS - Whole Genome Sequencing
  • MHC - Major Histocompatibility Complex
  • pMHC - Peptide-MHC Complex
  • TCR - T-cell Receptor
  • BCR - B-cell Receptor
  • HLA - Human Leukocyte Antigen
  • CDR3β - Complementarity-Determining Region Beta
  • TME - Tumor Microenvironment
  • RV - Reverse Vaccinology
  • TESLA - Tumor Epitope Selection Alliance
  • NGS - Next-Generation Sequencing
  • SNP - Single Nucleotide Polymorphism
  • Indel - Insertion or Deletion
  • AUC - Area Under the Curve
  • AUPRC - Area Under Precision-Recall Curve
  • TPM - Transcripts Per Million

User Guidelines

Strictly follow the file formats and naming conventions provided here to get your result :

  • Input paired-end FASTQ files should be named as: example_1.fastq.gz, example_2.fastq.gz
  • Find example paired-end sequencing files here : File1 File2
  • Input BAM file should be named as: example.bam
  • Find example bam file here
  • For TCR-peptide bindings, input should be a txt file with 2 columns, peptide followed by TCR regions separated by a tab. No headers required.
  • Find example TCR-peptide pair file here

If you have questions about additional terminology, please contact our support team at (debrajccds@kgpian.iitkgp.ac.in).