Pre-processed Genome Phage (gPhage ) - Trypanosoma cruzi

Input Datasets This directory contains the pre-processed files from the gPhage project, which serve as the input data for the EPIZAP pipeline to predict Trypanosoma cruzi epitopes recognized by the antibody response of Chagas disease patients. The dataset comprises eight individual sample files, representing two biological replicates (A and B) across four distinct clinical groups: Control: Healthy volunteers (Negative for Chagas disease) Asymptomatic: Patients with no EKG abnormalities Mild CCC: Patients with mild Chagas cardiomyopathy Severe CCC: Patients with severe Chagas cardiomyopathy List of Individual Sample Files: control_a, control_b, asympto_a, asympto_b, CCC_mild_a, CCC_mild_b, CCC_severe_a, CCC_severe_b Consolidated Files & File Integrity To streamline the pipeline execution, data across all patient groups have been merged into consolidated files. The table below provides the file details, total record counts, and MD5 checksums for data integrity verification prior to running EPIZAP. File Name Records MD5 Checksum Description DNA_inserts_all_patients_groups.fastq.zip 2,297,587 9fcc12426e2ebf6c520edc5dd42e818f Contains the merged coding DNA inserts from all eight clinical samples (compressed). DNA_insert_IDs_by_group.tsv.zip 2,297,587 785fb95877242e021d3b49772b5209aa Specifies which patient clinical group each DNA insert ID belongs to (compressed). peptides_encoded_by_DNA_inserts.fasta.zip 62,282 a3ac336dc898e18a5571e5851e40f9bb Contains the amino acid sequences of the unique peptides encoded by the DNA inserts (compressed). peptides_encoded_by_DNA_inserts.tsv.zip 62,282 29e64a654489eea63a33690d9fe067fe A tabular (.tsv) version of the peptide data, including sequence length information (compressed). DNA Insert to Peptide Mapping Importantly, the uniqueness of the peptides within the peptides_encoded_by_DNA_inserts is defined by their genomic origin (the specific coding DNA insert) rather than solely by their amino acid sequence. Due to the degeneracy of the genetic code, distinct nucleotide sequences can frequently encode structurally identical amino acid sequences. Therefore, each peptide is assigned a unique identifier (ID) that links it back to its originating DNA insert, preserving full traceability to the corresponding genomic sequence. This strict distinction is maintained throughout the entire processing pipeline. In practice, this relationship is established by the numeric suffix appended at the end of the DNA insert ID within the FASTQ file. For example, a DNA insert with the ID @M01677:61:000000000-AHLMU:1:1106:17399:9980_82653 encodes the peptide identified as 82653 (indicated by the _82653 suffix). You can find this exact corresponding sequence in the peptides_encoded_by_DNA_inserts.fasta file, structured as follows: >82653 TPTDEEKDWRRISRGGQFLAVGRGSTANWSKKPLKQVDQNVGN