RNA-Seq FAQ

Answers to frequently asked questions about RNA-seq analysis.

Where can I find and change the default trimming settings for an RNA-seq analysis?
When you are setting up your analysis, click on “Change Default Options.” This will display all analysis parameters that can be changed.  Scroll d...
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?
A PCA plot is a great way to find outliers. First and foremost, it gives you a starting point to try and figure out — why is that sample an outlier? That&#x...
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?
The Wald test is what's used by default for comparing 2 groups of samples in a differential expression analysis.  The LRT is the preferred method f...
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?
That’s right. Positively and negatively correlated refers to whether a set of genes are enriched, or upregulated, in the group. If the pathway is positively...
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?
No. At the moment, Basepair only accepts raw read files in BAM and FASTQ format. Still, we recommend you convert your BAM files to FASTQ format using our BA...
Thu, 8 Oct, 2020 at 5:57 PM
How can you tell the difference between enriched and not enriched GSEA plots?
note: at present, GSEA plots are not displayed directly in the Basepair report. To access GSEA plots, you’ll need to go into the Info tab at the top of the ...
Thu, 13 Aug, 2020 at 4:48 PM
What is a good alignment rate in the Expression Count report?
Whether an alignment rate can be considered "good" depends on the source and library prep kit used for the sample, so it can be difficult to assig...
Fri, 4 Dec, 2020 at 12:42 AM
In the differential expression report, which metric is more important: P-value or P-adjusted value?
The P-adjusted value is preferred in most cases because it accounts for the False Discovery Rate, or false positives. In some cases, the P-value can be used...
Mon, 17 Aug, 2020 at 6:04 PM
What is a good quality score?
The higher your quality score is, the better. As a reminder, the quality score graph is split into 3 different sections, which helps you easily identify whe...
Fri, 30 Oct, 2020 at 2:33 PM