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hello my name is michael weinstein im a bioinformatics scientist at zymo research as well as being a sequencing and ngs instructor at ucla and today im going to talk about some of the basics of dealing with your ngs output files so i think the two fundamental output formats youre going to get from just about any ngs application are going to be your raw reads and for that were going to talk about fastq files well also talk a little bit about qc because i wont mention they exist uh and then for the second major output its your alignment and thats going to come in the form of your bam files and your sam files and im going to give you an example of a sam file the only difference between bam and sam files the sam files are human readable bam files are compressed and theyre not but otherwise everything between them is the same so i will walk you through how to understand the various fields in these files understand how to go through them and understand what your sequencing data is
