CROP-Seq

Introduction

This section is for those starting their analysis of CROP-seq datasets. It will focus on taking your sequencing data to numerical data and show you how to install what you need, align your reads, and assign all cells carrying an sgRNA to their respective guide.

Overview

A brief overview of what you will do:

1. Prepare your environment for the analysis

   • Installation
   • Directory Management

2. Sequencing Alignment

   • Aligning to the transcriptome
   • Aligning to the sgRNA library

3. sgRNA Assignment

   • Statistically assigning cells to sgRNAs
   • Intersecting 10X and sgRNA library into a single dataset.

What to do next

From there you will be able to use other tutorials written elsewhere for the single-cell analysis.

Some helpful links to those below:

• scanpy