The adapters used in this assay are optimized for the AmpliSeq workflow. Nextera or TruSeq Adapters are not compatible with this assay.
See Contents & Storage.
It is possible to run 3 different AmpliSeq for Illumina designs each with barcodes on the same sequencing run. However, your target amplicon size and required coverage must be achieved in a single run.
A 2×151 bp paired-end read is recommended.
See Product Compatibility.
You can manipulate coverage by increasing sequencing throughput (eg, a larger flow cell output or sequencing platform) or reducing the number of samples pooled per run.
The RNA Amplicon analysis workflow can be used for differential expression analysis. The RNA Amplicon Analysis App is available on BaseSpace Sequence Hub. Local Run Manager has a similar RNA Amplicon Analysis Module which utilizes the same workflow and algorithm as the BaseSpace Sequence Hub Apps.
Yes, there are example data sets in BaseSpace Public Data.
On-target bases shows the percentage of total sequenced bases that map to target regions in the reference genome. This metric reflects the percentage of bases from amplicons that a) were designed, synthesized, and pooled and b) generated sequence data mapping to the target regions.