RNA-Seq FAQ (11)

Answers to frequently asked questions about RNA-seq analysis.

Where can I find and change the default trimming settings for an RNA-seq analysis?

Modified on Thu, 13 Aug, 2020 at 3:19 PM
I see what looks like an outlier sample in my PCA plot. What should I do? Should I exclude the sample from the analysis?

Modified on Thu, 8 Oct, 2020 at 5:55 PM
What is the difference between the Wald test and the Likelihood Ratio Test (LRT), and which is preferred?

Modified on Thu, 13 Aug, 2020 at 4:38 PM
What does it mean when a set of genes are positively correlated versus negatively correlated in the GSEA analysis? Does positively correlated mean those genes are upregulated in the sample?

Modified on Thu, 13 Aug, 2020 at 4:36 PM
I already completed some analysis of my data and have an expression matrix of read counts. Can I upload that data into Basepair for further analysis?

Modified on Thu, 8 Oct, 2020 at 5:57 PM
How can you tell the difference between enriched and not enriched GSEA plots?

Modified on Thu, 13 Aug, 2020 at 4:48 PM
What is a good alignment rate in the Expression Count report?

Modified on Fri, 4 Dec, 2020 at 12:42 AM
In the differential expression report, which metric is more important: P-value or P-adjusted value?

Modified on Mon, 17 Aug, 2020 at 6:04 PM
What is a good quality score?

Modified on Fri, 30 Oct, 2020 at 2:33 PM
Data normalization for RNA-Seq & Heatmap Generation

Modified on Sat, 10 Jul, 2021 at 8:48 AM