ASPRIN

Allele-Specific Protein-RNA Interaction

Requirements

ASPRIN is intended to be used in a Unix-based environment. It has been tested on Mac OS and Linux.

Working installations of Python, pysam and samtools are required.

Python packages fisher, progressbar and mne are also required.

Installation

All of the below installation instructions assume you have write access to the installation directory for ASPRIN; if you want to install into a central location for all users, you may need to prefix these with sudo.

Configure

Now type

./configure

If user does not have administrator level access, type:

./configure --prefix=/home/user/installation/path/

This will configure the installation. ASPRIN is written partially in Python. By default, it will use whichever python interpreter is invoked when you type 'Python' on the command line. If you wish to specify a different version of Python, you can do this when running the configure script. Additionally, if any of the required external software packages listed above are not on your path, you can specify their location when running configure. For example, to specify the path to python and all of the exeternal software packages, you would type the following:

./configure --with-python=/some/path/to/python

You can also set PYTHONPATH to augment search path for module files, with the same format as shell’s PATH. For more information, refer to:

https://docs.python.org/2/using/cmdline.html#envvar-PYTHONPATH

You needn't include them all, just the ones that cannot be found in your path. The configure script will tell you if any requirements cannot be found, in which case ASPRIN cannot be installed.

Install

After configuration, ASPRIN is installed by typing:

make install

This will install Python modules for whichever version of Python you are using.

Usage:

To run ASPRIN, 3 arguments have to be provided:

1. Either Single Nucleotide Variants (SNVs) file called from RNA-seq data independently or the genotype file obtained previously from any assay. In either case, the variants have to be obtained prior to running ASPRIN and should be in .vcf file format.

2. CLIP-seq data, mapped reads in .bam file format, sorted based on coordinates and indexed. Mapped reads are preferably from eCLIP assay, following the ENCODE eCLIP processing pipeline up to and before calling peaks.

3. RNA-seq data, mapped reads in .bam file format, sorted based on coordinates and indexed, following any RNA-seq mapping procedure of choice.

In addition, 4 optional arguments can be provided to filter SNVs and focus on variants of choice, or simply just label variants:

1. dbSNP VCF file: To be able to filter noise, focus on SNPs, or simply label the SNPs that are in the VCF file.

2. RADAR RNA editing database file: To focus or simply just lebel variants that are known RNA editing events.

3. Number of threads (the default value is 25)

4. -a option, to consider all the variants, even if dbSNP and RNA editing files are provided for labeling the variants.

    $ asprin [-h] [-g Single Nucleotide Variants (SNVs) file]
             [-c CLIP-seq mapped reads file]
             [-r RNA-seq mapped reads file] 
             [-s dbSNP VCF file]
             [-e RADAR RNA editing database file]
             [-t Number of threads default: 25] [-a]

    ASPRIN: Allele Specific Protein-RNA Interaction

    optional arguments:
      -h, --help            show this help message and exit
      -s dbSNP VCF file
      -e RADAR RNA editing database file
      -t Number of threads (default: 25)
      -a                    Use all the variants

    required arguments:
      -g Single Nucleotide Variants file
      -c CLIP-seq mapped reads file
      -r RNA-seq mapped reads file

Examples:

ASPRIN has 5 different modes of operation:

1. Running on all variants

    $ asprin -g example/HepG2_test_variants.vcf
             -c example/RBFOX2_HepG2_clip_test.bam
             -r example/HepG2_total_rnaseq_test.bam
             -o output_all.txt

2. Running on variants present in dbSNP only (SNPs)

    $ asprin -g example/HepG2_test_variants.vcf 
             -s example/dbsnp_test.vcf
             -c example/RBFOX2_HepG2_clip_test.bam
             -r example/HepG2_total_rnaseq_test.bam
             -o output_snps.txt

3. Running on variants present in RADAR only (RNA editing events)

    $ asprin -g example/HepG2_test_variants.vcf 
             -e example/radar_test.txt
             -c example/RBFOX2_HepG2_clip_test.bam
             -r example/HepG2_total_rnaseq_test.bam
             -o output_editing.txt

4. Running on variants in both dbSNP and RADAR

    $ asprin -g example/HepG2_test_variants.vcf
             -s example/dbsnp_test.vcf 
             -e example/radar_test.txt
             -c example/RBFOX2_HepG2_clip_test.bam
             -r example/HepG2_total_rnaseq_test.bam
             -o output_snps_and_editing.txt

5. Running on all variants but label the SNPs and RNA editing events:

    $ asprin -g example/HepG2_test_variants.vcf
             -s example/dbsnp_test.vcf 
             -e example/radar_test.txt
             -a
             -c example/RBFOX2_HepG2_clip_test.bam
             -r example/HepG2_total_rnaseq_test.bam
             -o output_all_labeled.txt

The example input and outputs are found in the folder called example.

dbSNP and RADAR databases:

dbSNP and RADAR under hg19 annotations databases can be downloaded from here:

dbSNP: ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/All_20180418.vcf.gz

RADAR: http://lilab.stanford.edu/GokulR/database/Human_AG_all_hg19_v2.txt

For other versions of the databases please visit dbSNP and RADAR websites.

Enjoy!

Contacts and bug reports

Emad Bahrami-Samani [email protected]

Yi Xing [email protected]

If you found a bug or mistake in this project, we would like to know about it. Before you send us the bug report though, please check the following:

1. Are you using the latest version? The bug you found may already have been fixed.
2. Check that your input is in the correct format and you have selected the correct options.
3. Please reduce your input to the smallest possible size that still produces the bug; we will need your input data to reproduce the problem, and the smaller you can make it, the easier it will be.

Copyright and License Information

Copyright (C) 2017 University of California, Los Angeles (UCLA) Emad Bahrami-Samani, Yi Xing

Authors: Emad Bahrami-Samani, Yi Xing

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.