Allelic expression analysis of Imprinted and X-linked genes from bulk and single-cell RNAseq data

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About BrewerIX

BrewerIX is a graphical application for Linux or macOS for the detection of loss of imprinting (LOI) and X chromosome status by analysing SNVs from raw sequencing data in FASTQ format.

It automatically downloads all the required software and reference SNV information (human and mouse available), and it analyses the data guiding the user thorough an intuitive interface.

When running BrewerIX, the user can choose among three analysis modes: standard, complete and tailored. The standard and complete mode run with pre-compiled set of SNVs: bi-allelic and bi-allelic plus multi-allelic, respectively. For the tailored mode, the user can provide her own set of SNVs in VCF format.

Results are saved in a text file called “brewer-table.txt” and shown to the user. Visualization can be changed according to user defined parameters. All the graphical output can be saved and results can be easily shared by the "brewer-table" that can be easily opened with the BrewerIX app of your collaborators.

Features

Only requires RNAseq data in FASTQ format
Design to explore imprinting status
Detect XCI erosion
Intuitive analysis set up
Application restart from leatest valid point
Highly shareable results
No bioinformatic skills required
Run on common desktops or laptops
Multiple processing cores
Reproducible
Transparent
Modular

Playground

Download this brewer-table to have a demonstration of BrewerIX capabilities and features.

If you want to go deeper, download our example dataset (5 samples - paired end).

If you need more!

If you need a more flexible, custom analysis, you can create your analysis using the command line interface!

Follow the Brewer on GitHub. Install the brewerix-cli Python Package and follow the tutorials! They will guide you to set up your analysis.

Code is open source under licence AGPL3.

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BrewerIX is freely available for academic use only.

macOS BrewerIX for macOS * (x64)
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Linux BrewerIX for Linux ** (x64)
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* You need to authorize the application on the first run

** Tested on Ubuntu 18.04, Ubuntu 20.04, Debian Buster, CentOS 7, CentOS 8 and Fedora 32

FAQs

Unfortunately not! You cannot use BrewerIX on Windows Systems because some analysis tools are not available for Windows.

Yes, you can do it using the brewerix-cli, but chromosome orders must be strictly identical to the VCF file!

You can use Human or Mouse in BrewerIX. If you need other organisms you have to run brewerix-cli. It’s pretty easy. Find out more in the tutorials in GitHub.

If you have an error, please contact us and send the latest saved log!

Yes, you can. The brewer-table and all the tabular output from BrewerIX are saved in tab-separated value and can be opened by any spreadsheet program.

To deal with Single Cell data (or a lot of samples in general) you need to summarize your experiment. In the paper we summarized experiments in categories. Follow the tutorials in GitHub to see how.

White dots in the gene summary means that no biallelic SNVs were found according to the set parameters

If you have no dots it means that we don’t have any single read overlapping any SNV in the sample. A grey square means that gene do not reach detection according to your thresholds

In BrewerIX, you can select the knowledge base at the very beginning of the analysis. If you need to specify your knowledge base you can create one using our tool and then run the analysis with brewerix-cli. The brewer-table can be explored by BrewerIX as well.

“Other” means all those SNVs that were included in the analysis but that are not from the source we curated. For example, when you run a tailored analysis and you use your own set of SNVs.

It depends on your setting. If you have an high coverage, we suggested the threshold. If you have a small coverage, we suggested the p-values.

No, BrewerIX is not meant to perform variant calling. It was devised to perform Allele Specific Expression Read Count at any give bi-allelic position. We include Haplotype caller step only to get bi-allelic sites out of multi-allelic sites

Please read the error message. If the solution in not obvious it means that there was an unexpected event and possibly a bug. Please submit a bug to our bug tracking system in GitHub along with the log file and a small reproducible example