Question about downstream terminology.

Question

[mangfu100]

Hi

I ask a question about term "downstream".

I know that downstream refers to the direction of 3'. That is all I have learned.

While reading below sentence, however, I am so confused that why the term "downstream" was used.

After mapping reads to the reference genome, a three step post-alignment processing procedure is recommended to minimize the artifacts that may affect the quality of downstream variant calling. It consists of read duplicate removal, indel realignment, and base quality score recalibration.

Base quality is a critical factor for accurate variant detection in the downstream analysis.

I fully understood above sentence except the downstream.

I cannot connect downstream I knew with the potential meaning in the sentence.

Could you help me why the term downstream was used for those sentence?

Answer 1

[Devon Ryan]

You might just want to look "downstream" and "upstream" up in a dictionary. These are generic English terms. But because I'm feeling nice this morning:

Imagine a river. Rivers flow in a single direction and if you placed something (that floats) in a river it would float with the current, passing by points along the coast in a set order (after all, it's not going to float against the current). If you were standing on the shore and the object were floating toward you, then it'd be upstream of you. After it passed you, it'd be downstream of you. In English, we generalize these terms to apply to any set of processes with a (roughly) linear ordering. So when you first get sequencing data, you'll probably perform some quality control steps and then alignment or assembly. These are the upstream-most steps. Once, that's done, the downstream steps (variant calling, counting alignments per gene in RNAseq, calling ChIP peaks, etc.) are performed, which generally is when the data starts getting more interesting.

[PoGibas]

+1 for being nice this morning :-)

[Devon Ryan]

Great, now I feel compelled to be nice all day :P