ContigExpress, LLC

Following is a list of common analysis items for RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project.

1) Experiment design consultation
2) Data QC and clean up
3) Alignment to a reference with mapping statistics
4) Gene and transcript-based quantitation, RPKM/FPKM-based quantitation, Raw hit count-based quantitation
5) Differential expression analysis with p-value and FDR: Pair-wise comparison, Time course analysis, Clustering, Principle component analysis
6) Enrichment, pathway, and Gene Ontology (GO) analysis
7) Novel splicing variant analysis
8) Gene fusion and other structural variant analysis
9) SNP discovery and characterization
10) Written project report with analysis methods, publication-ready graphics, and references

Following is a list of common analysis items for Methylation Sequencing, including MeDIP-Seq, hMeDIP-Seq, RRBS / Targeted Bisulfite-Seq, WGBS, and 5-mc RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project.

1) Experiment design consultation
2) Data QC and clean up
3) Methylation state-sensitive mapping
4) Methylation site calling
5) Gene assignment and methylation site annotation
6) Gene Ontology and pathway analysis
7) Written project report with analysis methods, publication-ready graphics, and references

Following is a list of common analysis items for ChIP-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project.

1) Experiment design consultation
2) Data QC and clean up
3) Alignment to a reference with mapping statistics
4) Peaking calling with or without control samples
5) Gene assignment and peak annotation
6) Data clustering and visualization
7) Motif analysis
8) Pathway and network analysis
9) SNP discovery
10) Written project report with analysis methods, publication-ready graphics, and references

Following is a list of common analysis items for Whole genome assembly. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project.

1) Experiment design consultation
2) Data QC and clean up
3) Contig assembly
4) Scaffolding and gap closure
5) Gene/ORF prediction
6) Gene annotation and classification via database search and comparison
7) Gene Ontology and pathway analysis
8) SNP discovery and analysis
9) Comparative genome analysis
10) Written project report with analysis methods, publication-ready graphics, and references

Following is a list of common analysis items for Whole Genome Resequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project.

1) Experiment design consultation
2) Data QC and clean up
3) Alignment to a reference with mapping statistics
4) Local realignment
5) SNP and small indel calling
6) SNP/small indel characterization
7) SNP-based genotyping
8) Association study and linkage disequilibrium analysis
9) Structural variation detection and characterization
10) Written project report with analysis methods, publication-ready graphics, and references

Following is a list of common analysis items for Targeted Resequencing and Exome Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project.

1) Experiment design consultation
2) Data QC and clean up
3) Alignment to a reference with mapping statistics
4) Local realignment
5) SNP and small indel calling
6) SNP/small indel characterization
7) Written project report with analysis methods, publication-ready graphics, and references

DNA Sequencing Services