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 |