Gene expression with assembly and without !!
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5.4 years ago
loly.pearl86 ▴ 30

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 ??cant 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

RNA-Seq Assembly sequencing • 1.0k views
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5.4 years ago
h.mon 32k

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.

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5.4 years ago
Chris Fields ★ 2.2k

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.

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Thanks all for u answers

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