File format

**FastQ**

>ReadID
READ SEQUENCE
+
SEQUENCING QUALITY SCORES

**BAM**

The human-readable version is called a SAM file, while the BAM file is the highly compressed version.
Alignment rows employ a standard format with the following columns:
QNAME : read name (generally will include UMI barcode if applicable)
FLAG : number tag indicating the “type” of alignment, link to explanation of all possible “types”
RNAME : reference sequence name (i.e. chromosome read is mapped to).
POS : leftmost mapping position
MAPQ : Mapping quality
CIGAR : string indicating the matching/mismatching parts of the read (may include soft-clipping).
RNEXT : reference name of the mate/next read
PNEXT : POS for mate/next read
TLEN : Template length (length of reference region the read is mapped to)
SEQ : read sequence
QUAL : read quality
BAM/SAM files can be converted to the other format using ‘samtools’