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?
<p>You might just want to look &quot;downstream&quot; and &quot;upstream&quot; up in a dictionary. These are generic English terms. But because I&#39;m feeling nice this morning:</p>

<p>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&#39;s not going to float against the current). If you were standing on the shore and the object were floating toward you, then it&#39;d be upstream of you. After it passed you, it&#39;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&#39;ll probably perform some quality control steps and then alignment or assembly. These are the upstream-most steps. Once, that&#39;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.</p>
