CITE-seq-Count
A tool that allows to get UMI counts from a single cell protein assay.
This pipeline wraps the CITE-seq-Count tool to run in Owl. Please follow the link to learn more about this tool.
Install
curl -O https://raw.githubusercontent.com/eddienko/owl-cite-seq-count-pipeline/main/owl_cite_seq_count/cite-seq-count.yml
owl admin pdef add cite-seq-count.yml
Pipeline Definition File
The pipeline definition file is:
# Version of the configuration file
version: 1
# Name of the pipeline
name: cite_seq_count
# Pipeline arguments
# Read1 fastq file location in fastq.gz format.
# Read 1 typically contains Cell barcode and UMI
read1: /storage/admin/cite/5kPBMC/big_R1.fastq.gz
# Read2 fastq file location in fastq.gz.
# Read 2 typically contains the Antibody barcode.
read2: /storage/admin/cite/5kPBMC/big_R2.fastq.gz
# The path to the csv file containing the antibody
# barcodes as well as their respective names.
tags: /storage/admin/cite/5kPBMC/tags.csv
# First nucleotide of cell barcode in read 1
cell_barcode_first_base: 1
# Last nucleotide of the cell barcode in read 1
cell_barcode_last_base: 16
# First nucleotide of the UMI in read 1
umi_first_base: 17
# Last nucleotide of the UMI in read 1
umi_last_base: 28
# How many cells you expect in your run
expected_cells: 6000
# How many bases should we trim before starting to map
trim: 10
# Output
output: /storage/admin/5kPBMC/output
# Extra arguments
# extra: ["--max-error", "3", "--no_umi_correction"]
# Resources requested
resources:
cores: 10
workers: 1
memory: 32