You may have heard that we have recently collaborated with Partek on a Single Cell Analysis Pipeline for the Nadia Instrument. This exciting collaboration will enable users to now analyze their single cell drop-seq data without any prior bioinformatics experience.
Single cell data analysis enables researchers to gain unprecedented understanding and insight into the heterogeneity of single cells and their biological state through a range of statistical visuals and plots. Once analysed this is key to understanding many diseases and immunity and is fundamental in a range of research applications.
With this software, Nadia derived single data can now be easily processed through Partek Flow to create user-defined data plots. Complex upstream data processing steps including sequence alignment, tag trimming, de-duplication, barcode identification and transcriptome quantification are automated within the software workflow providing insight to users of all experience.
- Import data – Start with FASTQ, BAM, or count matrix files, from single or multiple samples
- Trim tags – Automatically remove cell barcodes and UMIs
- Align reads – Align to the reference genome using industry standard RNA aligners
- Deduplicate UMIs – Remove PCR duplicates
- Post-alignment QA/QC – Filter to include only high-quality single cells
- Quantify to transcriptome – Generate a single-cell expression count matrix against an annotation model of your choice
- Perform downstream single-cell RNA-Seq analysis including QA/QC, filtering, normalization, clustering, sub-population classification, biomarker discovery and more
Once processed the single cell data can be visualized in a range of user-defined data plots to enable you to fully understand your single cell sample. The software can be used to create 3D t-SNE-plots to identify cell types and cell clusters or even pathway signatures, plus much more!
You can learn more about the Single cell analysis pipeline for the Nadia Instrument on the recording of our most recent webinar Single Cell Analysis – Using Partek Flow to seamlessly analyze Nadia data or download our flyer.
If you have any questions regarding this software and how it can be used with your single-cell data, contact us today