Inspection of BAM files

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Click on the small eye icon of a Bam dataset (generated either with RNA STAR or HISAT2)

The header contains the chromosome specifications (their name and length) and other informations such as the software that generation the Bam file and the command line to run the software.

A BAM file (or a SAM file, the non compressed version) consists of:

A header section (the lines starting with @) containing metadata, in particular the chromosome names and lengths (lines starting with the @SQ symbol) An alignment section consisting of a table with 11 mandatory fields, as well as a variable number of optional fields:

Col	Field	Type	Brief Description
1	QNAME	String	Query template NAME
2	FLAG	Integer	bitwise FLAG
3	RNAME	String	References sequence NAME
4	POS	Integer	1-based leftmost mapping POSition
5	MAPQ	Integer	MAPping Quality
6	CIGAR	String	CIGAR String
7	RNEXT	String	Ref. name of the mate/next read
8	PNEXT	Integer	Position of the mate/next read
9	TLEN	Integer	observed Template LENgth
10	SEQ	String	segment SEQuence
11	QUAL	String	ASCII of Phred-scaled base QUALity+33

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