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2.0 years ago
cwwong13
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40
I realized that the 10x workflow is the convention nowadays for making a single-cell library. However, when this technology is not as popular as today, pioneers, such as the protocol by Tang, et al used to capture the whole length of mRNA instead of using the UMI system.
When I was trying to search for a single-cell analysis workflow, the search results were flooded with the 10x version. I am not sure if the same pipeline, such as the Seurat R package can be used for these old datasets. Therefore, It would be great if anyone can point me to some resources that are suitable for analyzing single-cell RNAseq data without the UMI system. Thanks!
There are plenty of single-cell protocols that don't use UMIs (e.g. smart-seq2) -- you can look up the papers that use such protocols and see how they process the data.
You can use seurat/scanpy/whatever -- those downstream packages are designed to operate on gene x cell matrices (populated by gene counts). It doesn't matter whether it's 10X or something else.
The first step for you is getting a gene x cell matrix from an aligner. So, first, download the FASTQ files and then use an aligner (say, kallisto) to produce your gene counts.