Before Start

Important Note

YAP is a full pipeline designed for raw sequencing data (BCL files and raw FASTQ files before demultiplex) generated in the Ecker Lab.

If you download our published data and want to remap using the cell-level FASTQ files, I provided a tutorial here.

What is YAP?

YAP (Yet Another-Pipeline ) is a mapping pipeline designed for several single nucleus methyl-cytosine sequencing (snmC-seq) based technologies (see below).

It starts from demultiplexing FASTQ files and ends at generating single-cell ALLC files.

See source code on Github.

Technologies Supported

• snmC-seq2 & 3: DNA methylome

• snmCT-seq: DNA methylome + Transcriptome

• snm3C-seq: DNA methylome + Chromatin Contact

• NOMe treated: X + Chromatin Accessibility

How to use it?

1. Be familiar with the background of cell barcoding and the technology you use. If not, read the corresponding TECH BACKGROUND section.
2. Follow the installation tutorial to install yap and associated packages.
3. Follow the MAPPING PIPELINE section step by step.

4. If you have questions, first go to the FAQ page. If the problem is not solved, you can post an issue on GitHub.
5. This documentation is searchable.

After Mapping?

Check out ALLCools, the package for downstream cell-level and cluster-level analysis.

Authors

Hanqing Liu

Jingtian Zhou

Chongyuan Luo

Wei Tian