1. Services
2. FASTQ File Processing Service

If you have not done the experiment yet, please consider Premium Analysis Service. If you have numeric data files which are generated from FASTQ files, please consider Data Analysis Service. If you have problems on processing FASTQ files, please read below.

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Using bioinformatics tools is only the first step of NGS data analysis. Don't you think many researchers spend too much time only on the data processing? Don't you think you would better to spend time more on the interpretation and discovering?

Short-read sequencing technologies will be replaced by long-read sooner or later. And the next technology will also be replaced. At that time, tools and algorithms which are technology dependent will also be replaced. Why do you spend so much time on learning short-lived skills?

Subio Platform is independent from measurement technologies, and works as a platform for storing,comparing and integrating different types of data. The skills of carefully watching data, extracting biological insights and discovering the mechanism hidden behind are not temporary, but essential. This is what worth spending time to learn for biologists. We offer services on the technology dependent part.

Pipeline Setup Charge

Pipeline Setup charge is required per order.

mRNA-Seq Data Processing（Reference Genome）

This service deploys a pipeline with TopHat and Cufflinks to map reads and estimate the gene expression level. We add an extra fee for creating a custome genome, if it is not available.

mRNA-Seq Data Processing（De Novo Assembly）

We provide mRNA-Seq (de novo assembly) service at the fix rate. Assembled genes don't have annotation, and you'll need BLASTX to get biological information one by one. You know the top hit is not necessarily to be functionally related most. So we recommend building the annotation database for the assembled genes, which is not a simple table of top hits, but is a database keeping possible homologs.

ChIP-Seq Data Processing

This service deploys BWA and MACS. Genomes of human (hg19) and mouse (mm9 or mm10) are ready, and you can select one from the preset genomes. If you have data to map on other genomes, we can do it as a customized service, which cost depends on the organism and data/information you provide to us.

Variation Data Processing

SNV calling service based on GATK is available for human (hg19) and mouse (mm9 or mm10). Or maybe you already have VCF files, which are too large to work on Excel. VCF files can be visualized on for exploratory data mining. It's very helpful to examine the data quality, and find the points of analysis. And then you would filter variations, e.g. eliminating common variations to all samples or registered in dbSNP, or extracting variations with different frequencies between Normal vs. Tumor. We'll discuss about the criteria. If the number of variations becomes small enough, they can be visualized and analyzed on Subio Platform.