SCAPE-APA: a package for estimating alternative polyadenylation events from scRNA-seq data

Installation

Method 1

conda config --append channels bioconda 
conda config --append channels conda-forge 
conda config --append channels anaconda 
conda create -n scape_env python=3.11
conda activate scape_env

conda install anaconda::numpy
conda install anaconda::scipy
conda install anaconda::pandas
conda install anaconda::matplotlib
conda install anaconda::click
conda install anaconda::tomli-w
conda install anaconda::requests
conda install conda-forge::psutil
conda install conda-forge::tomli-w
conda install bioconda::bedtools
conda install bioconda::pybedtools
conda install bioconda::pysam
conda install bioconda::gffutils

pip install taichi
pip install scape-apa

Method 2

# Mac
conda env create -f mac_environment.yml
conda activate scape_env

Method 3

# Linux
conda env create -f linux_environment.yml
conda activate scape_env
pip install -r linux_requirements.txt

Method 4

# install locally
git clone https://github.com/chengl7-lab/scape.git
cd scape
pip install .

Commands

Command	Description
scape gen_utr_annotation	Generate UTR annotation.
scape prepare_input	Prepare data per UTR.
scape infer_pa	Parameters inference.
scape merge_pa	Merge PA within junction per gene or UTR.
scape cal_exp_pa_len	Calculate the expected length of PA.
scape ex_pa_cnt_mat	Extract read count matrix.

Get help information of scape or scape commands.

scape --help
scape gen_utr_annotation --help

Usage

gen_utr_annotation

Input Argument	Type	Required	Default	Description
--gff_file	TEXT	Yes	NA	The gff3 or gff3.gz file including annotation of gene body.
--output_dir	TEXT	Yes	NA	Directory to save dataframe of selected UTR.
--res_file_name	TEXT	Yes	NA	File Name of dataframe of the UTR annotation. The suffix .csv is automatically generated.
--gff_merge_strategy	TEXT	No	merge	Method for processing overlapping regions. It follows merge_strategy in package gffutils.

OUTPUT: An csv file including information of annotated 3UTR which is stored at {output_dir}/{res_file_name}.csv.

prepare_input

Input Argument	Type	Required	Default	Description
--utr_file	TEXT	Yes	NA	UTR annotation file (dataframe, resulted from gen_utr_annotation).
--cb_file	TEXT	Yes	NA	File of tsv.gz including all validated barcodes (by CellRanger). This file has one column of cell barcode which must be consistent with value of CB tag in bam_file file.
--bam_file	TEXT	Yes	NA	Bam file that is used for searching reads over annotated UTR.
--output_dir	TEXT	Yes	NA	Output directory to save pickle files of selected reads over annotated UTR.
--chunksize	INTERGER	No	1000	Number of UTR regions included in each small pickle file, which contains the preprocessed input file for APA analysis.

OUTPUT: Pickle files that include tuples (gene info, dataframe of parameter).

infer_pa

Input Argument	Type	Required	Default	Description
--input_pickle_file	TEXT	Yes	NA	Input pickle file (result of prepare_input)
--output_dir	TEXT	Yes	NA	Directory to save output pickle files including PAS information over annotated UTR.
--toml_para_file	TEXT	No	None	A TOML file (example) specifies user-defined parameters.
--pre_para_pkl_file	TEXT	No	None	A pickle file with pre-specified pA sites and utr length, result file of scape analysis.

OUTPUT: Pickle file including Parameters for each UTR region.

merge_pa

Input Argument	Type	Required	Default	Description
--output_dir	TEXT	Yes	NA	Directory which was used in previous steps to save output by prepare_input and infer_pa.
--utr_merge	BOOLEAN	No	True	If True, PA sites from the same gene are merge. Otherwise, if False, PA sites from the same UTR are merged.

OUTPUT: A single pickle file containing all UTRs of all genes is stored in output_dir/. Its name is res.gene.pkl if utr_merge=True, otherwise, its name is res.utr.pkl.

cal_exp_pa_len

Input Argument	Type	Required	Default	Description
--output_dir	TEXT	Yes	NA	Directory which was used in previous steps to save output by prepare_input and infer_pa.
--cell_cluster_file	TEXT	No	-	An csv file containing two columns in order: cell barcode (CB) and respective group (cell_cluster_file). Its name will be included in the file name of final result.
--res_pkl_file	TEXT	No	-	Name of res pickle file that contains PASs for calculating expected PA length. Its name will be included in the file name of final result.

OUTPUT: exp_pa_len.csv. It is a dataframe with 2 columns.

ex_pa_cnt_mat

Input Argument	Type	Required	Default	Description
--output_dir	TEXT	Yes	NA	Directory which was used in previous steps to save output by prepare_input and infer_pa.
--res_pkl_file	TEXT	No	-	Name of res pickle file that contains PASs for calculating expected PA length. Its name will be included in the file name of final result.

OUTPUT: An tsv.gz file named {res_pkl_file.cnt.tsv.gz} is stored in output_dir/.

Demo & Tutorials

The data used can be downloaded from examples.

• SCAPE toy example
• SCAPE example with differential expression analysis
• Benchmarks

Citation

Cheng G, Le T, Zhou R and Cheng L. SCAPE-APA: a package for estimating alternative polyadenylation events from scRNA-seq data [version 1; peer review: awaiting peer review]. Open Res Europe 2024, 4:220 (https://doi.org/10.12688/openreseurope.18673.1)