Understanding Raw NGS Data

How to read QSEQ, FASTQ, SAM, & BAM files from NGS analysis.

Code and computer CPU

For nearly every NGS analysis, the first two key steps are the generation of raw reads in the form of a FASTQ file and the alignment of those reads to a reference genome to create a SAM/BAM file. Understanding the details of how these files are written and what the different fields for each read mean can improve understanding of NGS analysis and the downstream applications that follow.

In the following video, learn about:

  • QSEQ vs. FASTQ files
  • Interpreting a read quality string
  • SAM vs. BAM files
  • Interpreting a Cigar string
  • Interpreting a Flag value