Active Motif: Your Custom Bioinformatics Solution
At Active Motif, our team of bioinformatic scientists has been providing premium bioinformatic analysis as part of our end-to-end Epigenetic Services for more than a decade. Now, we're offering this expertise for our customers who just require assistance with their bioinformatics. Perhaps you sent your samples away for sequencing and now don’t know where to begin with your delivered sequencing files. Aren’t sure how to move forward? We can help. Active Motif is providing customized bioinformatic analysis for ChIP-seq, ATAC-seq, DNA methylation, CUT&Tag, CUT&RUN, Hi-C, RNA-Seq, and single-cell analysis.
Here's what we do:
- Start with Your Data: Begin your project by uploading your FASTQ files.
- Alignment: Our team performs alignment, creating BAM (binary alignment map) files, BED (browser extensible data) files, and bigwig files as required for your experiment.
- Custom Comparisons: We handle all the necessary comparisons according to your specifications.
- In-Depth Analysis: You'll receive additional figures and statistical analyses to enhance your research insights.
Get practical, customized bioinformatics support from Active Motif. Let's turn your data into valuable discoveries.
Active Motif Bioinformatics Services for:
Active Motif Services
Full bioinformatic analysis is included with all Active Motif Epigenetics Services.
We can perform analysis and data integration on your experiments not limited to our own kits and services. Let us know what you need and we may be able to help accomplish your bioinformatics needs.
Ready to submit your FASTQ files? Let our team help.
Our Bioinformatic Workflows resulting in Comprehensive Reports
Click on the service to view the bioinformatic workflow:
CUT&RUN and ATAC-Seq
(Click image to enlarge)
What is a FASTQ file?
A FASTQ file is a common file format used to store DNA or RNA sequencing data, specifically the raw sequence reads generated by high-throughput sequencing instruments. FASTQ files contain information about the sequence of nucleotides and their associated quality scores for each base in a read. This format is widely used because it encapsulates both the sequence data and the quality information in a compact and standardized manner.
What is alignment and what software is used?
Alignment refers to the process of mapping or aligning short DNA sequences (reads) obtained from high-throughput sequencing experiments to a reference genome or transcriptome.
Many alignment tools are available including:
- Bowtie/Bowtie2: Bowtie and Bowtie2 are fast and memory-efficient aligners primarily used for mapping short reads (e.g., from Illumina sequencing) to reference genomes.
- BWA (Burrows-Wheeler Aligner): BWA is a widely used aligner that can perform both short-read and long-read alignments to reference genomes. It supports various mapping algorithms, including BWA-MEM for long reads and BWA-ALN for short reads.
- STAR (Spliced Transcripts Alignment to a Reference): STAR is a highly efficient aligner designed specifically for RNA-seq data. It can align reads to reference genomes while considering splicing events.
What is peak calling and what software is used?
Peak calling is a computational technique used in genomics and bioinformatics to identify regions of interest, often referred to as "peaks," in large-scale sequencing datasets. These peaks represent locations in the genome where specific biological events or signals are significantly enriched compared to background noise. Peak calling is essential for analyzing sequencing data in ChIP-Seq, ATAC-seq, and CUT&Tag.
Peak calling in ChiP-Seq and ATAC-Seq:
- ChIP-seq Peak Calling: In ChIP-seq experiments, researchers study interactions between proteins (such as transcription factors or histones) and DNA. The goal is to find regions in the genome where these proteins are bound. Peak calling in ChIP-seq identifies the specific genomic locations where the protein-DNA interactions occur, revealing potential binding sites.
- ATAC-seq Peak Calling: ATAC-seq measures the accessibility of chromatin, indicating which parts of the genome are more "open" and accessible for transcription factors and other proteins. Peak calling in ATAC-seq identifies regions with significantly higher chromatin accessibility, potentially pinpointing regulatory elements like enhancers and promoters.
Commonly used tools for peak calling in these types of experiments include:
- MACS2 (Model-based Analysis of ChIP-Seq 2): MACS2 is a popular tool for peak calling in ChIP-seq data. It uses a statistical model to find significant peaks of protein-DNA binding.
- SICER (Spatial Clustering for Identification of ChIP-Enriched Regions): SICER is designed for ChIP-seq data and identifies enriched regions using spatial clustering.
What is a bigwig file and how can I look at the trace?
A BigWig file is a binary file format used to store large-scale data, such as genome-wide data from next-generation sequencing experiments like ChIP-seq, ATAC-Seq, and DNA methylation data. This format is particularly useful for representing quantitative data, such as signal intensities or read counts, along a genomic coordinate system.
There are many tools that can be used to view and visualize the contents of a BigWig file. Here are two popular options:
- IGV (Integrative Genomics Viewer): IGV is a widely used genome browser that supports the visualization of BigWig files. You can download IGV from its official website (https://software.broadinstitute.org/software/igv/), load your BigWig file into it, and navigate through the genome to explore the data.
- UCSC Genome Browser: The UCSC Genome Browser (https://genome.ucsc.edu/) is another powerful tool. BigWig files hosted on a server can be uploaded to the UCSC Genome Browser website and visualized within the browser.
You can read more in our FASTQ blog article.
End-to-End Epigenetics Services
Prefer a complete solution? Send us your samples and we'll perform all the experimental steps, including sample prep, generating libraries, sequencing, bioinformatics analysis and delivery of data analysis and publication-ready figures. Check out our full Epigenetics Services for more information.
Popular End-to-End Services:
ChIP-Seq services for Histone PTMs and Transcription Factors with Spike-In Normalization. End-to-end service from sample prep to bioinformatics.
End-to-End services for genome-wide profiling of open chromatin regions from cell lines, primary cells, and tissue samples.
Whole-genome and gene-targeted analysis. RRBS, MeDIP/hMeDIP, bisulfite sequencing, and 5-fC/5-caC profiling.
View All Epigenetic Services