File Format Specifications – PanKbase

This document provides an overview of required formats for the different file types hosted by PanKbase.

Sequencing Data

• Format: .fastq
• Description: The .fastq format is an accepted standard for raw sequencing reads.
• Specification: FASTQ Format – maq.sourceforge.net

Sequence Alignments

• Format: .bam
• Description: Binary format for storing sequence alignments.
• Specification: BAM Format – samtools.github.io

Normalized Genomic Signal

• Format: .bigWig
• Description: Used for storing dense, continuous data such as coverage tracks.
• Specification: bigWig Format – UCSC Genome Browser

Gene Quantifications

• Format: Tab-delimited text
• Description: Contains gene or transcript-level counts and normalized expression values (e.g., from bulk RNA-seq).
• Specification: GTEx Gene Quantifications Format

Gene Count Matrix

• Format: Not specified
• Description: Matrix of gene expression values across multiple samples or cells.

QTL Summary Statistics

• Format: Tab-delimited text
• Description: Results from QTL mapping (e.g., eQTL, caQTL).
• Specification: To be added

Genetic Association Summary Statistics

• Format: Tab-delimited text
• Description: Results from GWAS or other genetic association analyses.
• Specification: To be added

Gene Sets

• Format: .gmt (Gene Matrix Transposed)
• Description: Lists of genes grouped by pathway, function, or disease association.
• Specification: GMT Format – Broad GSEA Wiki