Ask for help! Need a tutorial for processing Drop-seq data and converting sequencing data into expression matrix.

Question

[lyxwyc777]

Recently, I am processing a series of single-cell RNA sequencing raw data generated by the Drop-Seq platform in the format of .sra files downloaded on NCBI.

The data cannot be constructed into an expression matrix for R package Seurat analysis through many methods.

I hope to find a good method and tutorial for constructing an expression matrix using data from the Drop-Seq platform in scRNA-Seq.

[ektavpathak]

I am working on GEO dataset having scRNA-Seq form Drop-seq platform. It has 3 samples. I have the two Fastq file for each sample. I also wish to know how to get the expression matrix.

Have you got any method or pipeline for that. can we use cell ranger(although it is for 10X genomic)? Can anyone suggest.

Answer 1

[rpolicastro]

The Broad Institute github has software and a detailed vignette from the McCarroll for analysis of Drop-seq.