Basepair Support

When you are setting up your analysis, click on “Change Default Options.” This will display all analysis parameters that can be changed.  Scroll d...

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...

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 fo...

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...

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...

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 ...

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...

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...

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...

Data normalization for RNA-Seq The raw read counts are normalized using DESeq2 package. DESeq2 performs an internal normalization where geometric mean i...