caramirezal/SNARE_prep

dropseq-based single nuclei genomic accessibility and RNA expression (SNARE-seq) preprocessing pipeline

SNARE_prep

The pipeline to process chromatin accessibility data from DropSeq-based Single Nuclei genomic Accessibility and RNA Expression-seq (SNARE-seq) experiment.

Dependency

Drop-seq_tools-1.13/Picard

ATAC-seq pipeline

Reference(mm10,hg38)

.dict file

pysam

fastx_trimmer

Read(fastq) Structure

Read1(30 bp): [12-bp barcode][9-bp UMI]TTTTTTTTT

Read2(75 bp): Nextera Read1

Read3(75 bp): Nextera Read2

Usage

SNARE_Prep.sh -n $name -s $species -c $cells