What are the applications of read-reference sequence mapping?

Question

[manetsus]

I saw, like minimap, there are some tools which map read to reference sequence. But I want to know, what is the purpose of this work as I have the reference already?

I know, from read to read mapping, we could align and construct reference sequence using different tools.

Answer 1

[harold.smith.tarheel]

Here are a few of the many applications:

1) variant calling 2) gene expression 3) DNA binding 4) chromatin modification 5) chromosome conformation

[manetsus]

could you please add one or two lines in each of them briefing what they do actually?

[harold.smith.tarheel]

Have you tried searching the web? I'm sure you'll find descriptions of each of these applications without much effort.

[manetsus]

I could get the concepts easily. But the problem is, I could not relate them with read-reference mapping. Could you please help me to relate them by specifying that exactly where read-reference mapping is needed?

[harold.smith.tarheel]

For variant calling, you need to compare your data to a reference to identify sequence differences. For gene expression/DNA binding/chromatin modification, you need to count the number of reads at different genes/target loci. For chromosome conformation, you need to determine which loci are physically interacting. All of these applications require mapping to a reference.

[GenoMax]

One needs to take into account "support" (depth/number of reads piling up in the region after alignment) for a particular observation when doing any of the things originally listed by @Harold. This requires reference/read maps.