Inspection of BAM files


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