Post-experiment Service

  • Raw data quality control

Quality control raw data to ensure expected quantity and quality of sequencing data is met;

Contact sequencing service institution for necessary additional sequencing run.

  • Raw data filter

Low quality sequencing data are removed to ensure the quality of downstream data analysis. For certain tasks, special treatment will be performed (exp. Circular adaptor)

  • Data analysis

Sequence assembly and annotation: Genome or transcriptome assembly and annotation, the result will be in .fasta format for further analysis;

Sequence variation analysis: Report sequence variation (SNP/SNV, mutation and etc.) in standard .bcf or .vcf format or customized format for pipeline integration;

Genotyping: Recalibrate base call quality; Report genotype in genotype likelihood;

Gene expression quantification: Quantify gene expression count data in the form of raw count, reads per kilo base per million reads (rpkm) or count per million (cpm); Report gene expression in .txt, .csv, .tsv, or .xlsx format.

Statistical test for gene differentially expression: Provide raw statistical test result and filtered result based on standard cutoff.

  • Post data analysis

Genome browser configuration: Configure genome browser to host custom genome and gene model and genome sequence comparison with other genome model system; Launch genome browser in user-provided URL;

Genome hosting/Data storage: Host user’s custom genome, gene model; configure data server to store users’ data;


Discover regulation for mechanism and function interpretation from big dataset;

Correlation/Gene Set Enrichment Analysis;

Report variation cluster in custom format;

In silico up-stream regulator/drug prediction;

Discovery of potential up-stream effector gene (exp. Transcription factor, proteins modification and interaction); Report result in tabular format and network;

Machine/Statistical learning: Distinguish gene expression signature and apply the signatures for sample classification/diagnosis. Report result in tabular format and ROC;

Data mining: Public data mining requested by users. Data source includes TCGA, ENCODE, Ensembl, NCBI, 1000 Genome Projects and etc.

  • Publication support

Upload dataset to data repository (i.e. GEO, SRA);

Acquire accession number and setup data release date;

Draft relevant methodology for manuscript;