Gene expression with assembly and without !!

Question

[loly.pearl86]

Hi every one,

I am new in bioinformatic and NGS field .So I have some points which I confused in and hope to find some answers.

First: when we study gene expression why some times we do assembly after sequencing then qrt-pcr and some times only sequencing and qrt-pcr? I can't understand this point

Second:Why when we study gene expression some times we do biological replication when we do sequencing and some times without biological replications?!

Thanks

Answer 1

[h.mon]

As for your second question: biological replicates are fundamental to have good results (less false positives and better statistical power), but often times budget constraints and / or bad design decisions lead to studies without biological replication.

Answer 2

[Chris Fields]

h.mon answered the second question well. On the first question: it depends? It's kinda hard to say based on what info you give. For instance, if there is a (reliable) genome available you can run alignment and perform DGE analysis, whereas if the reference genome is poor or nonexistent you would need to run a transcriptome assembly prior to alignment and analysis. Some folks do both (except maybe use a reference-guided assembly instead of running a de novo one.

[loly.pearl86]

Thanks all for u answers