Services
RNA Sequencing
- Study design: Samples, Library prep protocol, Sequencing depth, Sequencing provider.
- Quality Control: QC of the raw FASTQ data
- Sequence Alignment: BAM file, Data Summarization, IGV Visualization
- Expression Quantification: FPKM, TPM, Sample Correlations.
- Differential expression analysis: Up-regulated and down-regulated genes.
- Gene ontology and pathway analysis: Enriched gene ontology and pathways.
- De novo transcriptome assembly: de novo mRNA assemblies.
- Novel mRNA, microRNA, lncRNA, circRNA, tsRNA: Novel transcript identifications by comparing with ENSEMBLE/RefSeq gene annotations.
DNA Sequencing
- WES, WGS, or Target Enrichment Sequencing
- Study design: Samples, Library prep protocol, Sequencing depth, Sequencing provider
- Quality Control: QC of the raw FASTQ data
- Sequence Alignment: BAM file, Data Summarization, IGV Visualization
- On target and off-target: on-target rate, Uniformity, Duplication reads
- Variant calling: SNPs and INDELs calling
- Variant calling and annotations: Annovar, ClinVar, OMIM, etc.
- Somatic mutations
- Copy Number Variations
Epigenetics Sequencing
- Bisulfite Sequencing: WGBS, RRBS, oxBS
- Study design: Samples, Library prep protocol, Sequencing depth, Sequencing provider
- Quality Control: QC of the raw FASTQ data
- Sequence Alignment: BAM file, Data Summarization.
- Methylation analysis: C to T convertion rate, methylation for CpG, CHG, CHH.
ATAC-Seq
- Study design: Samples, Library prep protocol, Sequencing depth, Sequencing provider.
- Quality Control: QC of the raw FASTQ data
- Sequence Alignment: BAM file, Data Summarization, IGV Visualization.
- Duplicate reads.Insert size of the library.
- chrM reads.
- TSS score and Blacklist peaks,
- Peaking calling: chromatin structure.
- Peak annotations and interpretations.
Ribosome profiling
- Ribo-Seq and RNA-Seq
- Study design: Samples, Library prep protocol, Sequencing depth, Sequencing provider.
- Quality Control: QC of the raw FASTQ data
- Sequence Alignment: BAM file, Data Summarization, IGV Visualization.
- Ribosome protected fragments.
- Three-nucleotide periodicity.
- Translation Efficiency for each gene.
- Differentially Translation Efficiency changed gene analysis.
Single Cell Sequencing
- Single Cell RNA-Seq and Single Cell ATAC-Seq
- Study design: Samples, Library prep protocol, Sequencing depth, Sequencing provider.
- Quality Control: QC of the raw FASTQ data
- Sequence Alignment: BAM file, Data Summarization, IGV Visualization.
- Duplicate reads.
- Number of cells.
- Number of genes.
- Raw read counts and clustering analysis.
- Peak calling from ATAC-Seq
Long Read Sequencing
- PacBio Sequencing and Nanopore Sequencing
- Study design: Samples, Library prep protocol, Sequencing depth, Sequencing provider.
- Quality Control: QC of the raw FASTQ data
- Sequence Alignment: BAM file, Data Summarization, IGV Visualization
- Customerized data analysis