Design Project

Query

A sequence read presented to an aligner; typically, a subsequence of an entire read (subread), which is basecalls from a single pass of the insert DNA molecule

Binary alignment and map = BAM file

• Binary format, not human-readable.

• More efficient: smaller size, faster computation, reduced storage costs.

• Almost all tools expect BAM input.

• Must be sorted (by read ID or genomic coordinates) and indexed (BAI file) before use.

Sequence alignment and map = SAM files

• Contains alignment info of mapped (against the reference genome) and unmapped sequences.

• Text-based, human-readable.

BAM Index = BAI

• Companion file, much smaller.

• Acts like a “table of contents” for BAM.

• Must be regenerated after sorting.

• Required by most analysis software.

Contig

= a set of overlapping DNA segments that together represent a consensus region of DNA

How are you going to investigate the methylation status?

IGV: Integrative Genomics Viewer