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in the above subsections, we introduced the basic concepts of the flow signals and how they are generated and stored in the bam file. the following section discusses more specific aspects of the data processing.
the file format for the raw flow signals is sam (sequence alignment/map). the sam format is a binary format for storing the alignment of reads to a reference. it contains the following fields: 1) header, 2) ns, 3) qx, 4) nm, 5) id, 6) qa, 7) gc, 8) sa, 9) ta, 10) qs, 11) ca, 12) qe, 13) qd, 14) qc, and 15) ns. the header provides information about the source file, project, the person who submitted the file, the date of the submission, the version of the software used to generate the file, and other information. the variant table stores information about the alignment to the reference genome and calls the variants for each sample. this is an important file that contains information about the snp sites for each sample. to make use of this file in downstream analysis, it is necessary to read the raw data into a database. this is done by loading the data into an sql database. each nucleotide change (e.g., a is changed into c) is stored in a row in the variant table and each row is represented by a vcf file. the next section provides an introduction to the commonly used alignment tools, especially the bwa (burrows-wheeler aligner) and stampy tools. the bwa tool has been chosen to be used in this study, because it is one of the widely used alignment tools and because it can align reads against the genome and against rrna sequences simultaneously. it is also one of the most recent alignment tools, and it is compatible with the latest version of the bioinformatics pipeline, samtools.
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