The "Post-PCR Clean and Sequence" service is for end users that wish to send CRUDE PCR samples. This charge is for PCR purification and one primer reaction.  For additional primers on the the same construct, please use "purified DNA for Sanger seqeuncing". 

Customized service to be discussed with the bioinformatics team

Price based on time spent for analysis ($75/hour)

Type of projects example:

Bioinformaticcs: Microarray analysis, GWAS, Population genetics & genomics, Demultiplexing

Biostatistics: Machine learning/ Statistical learning application, Power analysis, Survival Analysis, ANOVA, Rgression analysis, Dimensional reduction, mixed model, Biomarker identification, and etc

The "Clean and Load" sample service is for end users that have already run their own BIG DYE reaction prior to submission. 

Demultiplexing

FastQ file generation from NextSeq run for QC

DataReturn

Price per project

De novo genome assembly involves QA/QC and construction of draft genomes/contigs

Gene annotation includes gene prediction (e.g, coordinates of exons and coding regions) and functional annotation (e.g. gene identity and function).

*

Denovo transcriptome assembly from RNAseq data, including QA/QC, assembly, transcripts abundance estimation, DE genes detection, function annotation and evaluation of assembly quality.

Taxonomical analysis includes taxomony profiling and statistical analysis of biodiversity on species taxonomies or operational taxonomic units.

De novo genome assembly involves QA/QC and construction of draft genomes/contigs.

Gene annotation includes gene prediction (e.g., coordinates of exons and coding regions) and functional annotation (e.g. gene identity and function).

Microbiome Analysis for 16S rRNA sequencing, including taxonomic profiling, phylogenetic reconstruction, Alpha / Beta diversity, PCA plots and etc.

Microbiome Analysis for 16S rRNA sequencing, including taxonomic profiling, phylogenetic reconstruction, Alpha / Beta diversity, PCA plots and etc..

price: per sample

Microbiome Analysis for 16S rRNA sequencing, including taxonomic profiling, phylogenetic reconstruction, Alpha / Beta diversity, PCA plots and etc..

The "Post-PCR Clean and Sequence" service is for end users that wish to send CRUDE PCR samples. This charge is for PCR purification and one primer reaction.  For additional primers on the the same construct, please use "purified DNA for Sanger seqeuncing". 

Transcript quantification involves QA/QC, read alignment, peak calling, quantification and normalization. The output file contains information on the identity and quantity of each detected isoform of known transcript as annotated in the NCBI RefSeq or ENSEMBL database.

Novel transcripts that are detected in the samples but not annotated in the NCBI/ENSEMBLdatabase are also included in the output file.

DEG analysis is performed on each transcript with appropriate statistical test and correction for multiple comparisons.

Pathway analysis includes enrichment analysis that reports statistical significance for common pathways (e.g., KEGG pathways).

Transcript quantification involves QA/QC, read alignment, peak calling, quantification and normalization. The output file contains information on the identity and quantity of each detected isoform of known transcript as annotated in the NCBI RefSeq or ENSEMBL database.

DEG analysis is performed on each transcript with appropriate statistical test and correction for multiple comparisons.

Pathway analysis includes enrichment analysis that reports statistical significance for common pathways (e.g., KEGG pathways).

Same service as RNA-Sequencing (Standard) with both host and pathogen detected

Single-Cell Sequencing Analysis include: single-cell RNAseq and ATACseq.

Call variants involves QA/QC, read alignment, and variant detection. The output file contains information on position, reference allele, alternative allele, read counts, allele fraction and quality score for each called variant on nucleotide level.

Functional annotations include information on amino acid changes, functional significance predicted by SnpEff, ANNOVAR (including PolyPhen-2, SIFT and MutAssessor) and CHASM, frequency in the 1000 Genomes Project, COSMIC, TCGA and ICGC database, GeneOntology, pathways and potential bioassays and compounds in PubChem.

Call variants involves QA/QC, read alignment, and mutation detection. SNPs include substitutions, insertions and deletions. INDELs include small insertions and deletions (<50bp). SVs include copy number variants, translocations and other types of variants with length >50bps. The output file contains information on the reference allele, alternative allele, read counts and quality score for each called mutation on nucleotide level.

Functional annotations include information on amino acid changes, functional significance predicted by SnpEff.

Exons & 5’-UTR, resequencing a single eurokaryotic species, call mutations involve QA/QC, read alignment, and germinal/somatic mutation detection. The output file contains information on position, reference allele, alternative allele, read counts, allele fraction and quality score for each called mutation on nucleotide level.

Exons & 5’-UTR, resequencing a single eurokaryotic species, functional annotations include information on amino acid changes, functional significance predicted by SnpEff, ANNOVAR (including PolyPhen-2, SIFT and MutAssessor) and CHASM, frequency in the 1000 Genomes Project, COSMIC, TCGA and ICGC database, GeneOntology, pathways and potential bioassays and compounds in PubChem.

Single-Cell Sequencing Analysis include: single-cell RNAseq and ATACseq.

Customized service to be discussed with the bioinformatics team

Price based on time spent for analysis ($75/hour)

Type of projects example:

Bioinformaticcs: Microarray analysis, GWAS, Population genetics & genomics, Demultiplexing

Biostatistics: Machine learning/ Statistical learning application, Power analysis, Survival Analysis, ANOVA, Rgression analysis, Dimensional reduction, mixed model, Biomarker identification, and etc

Transcript quantification involves QA/QC, read alignment, peak calling, quantification and normalization. The output file contains information on the identity and quantity of each detected isoform of known transcript as annotated in the NCBI RefSeq or ENSEMBL database.

DEG analysis is performed on each transcript with appropriate statistical test and correction for multiple comparisons.

Pathway analysis includes enrichment analysis that reports statistical significance for common pathways (e.g., KEGG pathways).

Transcript quantification involves QA/QC, read alignment, peak calling, quantification and normalization. The output file contains information on the identity and quantity of each detected isoform of known transcript as annotated in the NCBI RefSeq or ENSEMBL database.

Novel transcripts that are detected in the samples but not annotated in the NCBI/ENSEMBLdatabase are also included in the output file.

DEG analysis is performed on each transcript with appropriate statistical test and correction for multiple comparisons.

Pathway analysis includes enrichment analysis that reports statistical significance for common pathways (e.g., KEGG pathways).

Same service as RNA-Sequencing (Standard) with both host and pathogen detected

Call variants involves QA/QC, read alignment, and mutation detection. SNPs include substitutions, insertions and deletions. INDELs include small insertions and deletions (<50bp). SVs include copy number variants, translocations and other types of variants with length >50bps. The output file contains information on the reference allele, alternative allele, read counts and quality score for each called mutation on nucleotide level.

Functional annotations include information on amino acid changes, functional significance predicted by SnpEff.

Denovo transcriptome assembly from RNAseq data, including QA/QC, assembly, transcripts abundance estimation, DE genes detection, function annotation and evaluation of assembly quality.

De novo genome assembly involves QA/QC and construction of draft genomes/contigs

Gene annotation includes gene prediction (e.g, coordinates of exons and coding regions) and functional annotation (e.g. gene identity and function).

*

Taxonomical analysis includes taxomony profiling and statistical analysis of biodiversity on species taxonomies or operational taxonomic units.

De novo genome assembly involves QA/QC and construction of draft genomes/contigs.

Gene annotation includes gene prediction (e.g., coordinates of exons and coding regions) and functional annotation (e.g. gene identity and function).

Microbiome Analysis for 16S rRNA sequencing, including taxonomic profiling, phylogenetic reconstruction, Alpha / Beta diversity, PCA plots and etc..

price: per sample

Microbiome Analysis for 16S rRNA sequencing, including taxonomic profiling, phylogenetic reconstruction, Alpha / Beta diversity, PCA plots and etc..

Microbiome Analysis for 16S rRNA sequencing, including taxonomic profiling, phylogenetic reconstruction, Alpha / Beta diversity, PCA plots and etc.

Call variants involves QA/QC, read alignment, and variant detection. The output file contains information on position, reference allele, alternative allele, read counts, allele fraction and quality score for each called variant on nucleotide level.

Functional annotations include information on amino acid changes, functional significance predicted by SnpEff, ANNOVAR (including PolyPhen-2, SIFT and MutAssessor) and CHASM, frequency in the 1000 Genomes Project, COSMIC, TCGA and ICGC database, GeneOntology, pathways and potential bioassays and compounds in PubChem.

Exons & 5’-UTR, resequencing a single eurokaryotic species, call mutations involve QA/QC, read alignment, and germinal/somatic mutation detection. The output file contains information on position, reference allele, alternative allele, read counts, allele fraction and quality score for each called mutation on nucleotide level.

Exons & 5’-UTR, resequencing a single eurokaryotic species, functional annotations include information on amino acid changes, functional significance predicted by SnpEff, ANNOVAR (including PolyPhen-2, SIFT and MutAssessor) and CHASM, frequency in the 1000 Genomes Project, COSMIC, TCGA and ICGC database, GeneOntology, pathways and potential bioassays and compounds in PubChem.

Demultiplexing

FastQ file generation from NextSeq run for QC

DataReturn

Price per project

The "Clean and Load" sample service is for end users that have already run their own BIG DYE reaction prior to submission. 

The "Post-PCR Clean and Sequence" service is for end users that wish to send CRUDE PCR samples. This charge is for PCR purification and one primer reaction.  For additional primers on the the same construct, please use "purified DNA for Sanger seqeuncing". 

The "Post-PCR Clean and Sequence" service is for end users that wish to send CRUDE PCR samples. This charge is for PCR purification and one primer reaction.  For additional primers on the the same construct, please use "purified DNA for Sanger seqeuncing".