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Data Deliverables

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Typical Deliverables

Depending on the sequencing technology, project type and amount of bioinformatics support required, the deliverables will differ.  In general this includes:

  1. Sequencing Report (MS Word file) – a written report documenting the performance of the sequencing job.
  2. FastQC Report (HTML file) – reports generated by a NGS data quality control tool which can be viewed on a web browser (Illumina Sequencing only).  Visit the author’s website for details.
  3. Analysis Report and Results (various file types) – reports summarizing the analyzed data and the analysis pipeline applied.  Project-specific analysis result files are also included (see below table).
  4. Intermediate analysis files (various file types) – files that are created throughout analysis, e.g. filtered high-quality reads in Fastq format.  Deliverables depend on project type (see below table).

Please choose the type of sequencing technology below to view the deliverables.
 

Illumina HiSeq Sequencing

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Illumina MiSeq Sequencing

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PacBio Sequencing

[ Bioinformatics Data Deliverables ]   [ Bioinformatics Data Deliverables ]   [ Bioinformatics Data Deliverables ]
Illumina HiSeq 2000   Illumina MiSeq   Pacific Biosciences

The Pacbio Sequel system is going on board at CGS soon, tentatively in June 2017.  Stay tuned!






Illumina HiSeq / MiSeq Sequencing - Specific Deliverables Based On Project Type

For analysis needs beyond our routine analysis pipeline (standard deliverables), customized assistance could be provided (custom deliverables). Please note that the list below is by no means an exhaustive list of deliverables possible. Do contact us if you cannot locate what you need. Final deliverables are subjected to mutual agreement between CGS and users.

Type of Project Standard Deliverables Custom Deliverables

RNA-Seq (mRNA)

Alignment Files in BAM format
Gene / Transcript Expression Level File in MS Excel format
*List of Differentially Expressed Gene / Transcript in MS Excel format (includes integration into Partek Genomics Suite for downstream pathway analysis)

*Includes 1 pairwise comparison for every 2 samples submitted for sequencing.  Additional comparisons are welcome, please contact us for details.

List of Annotated SNP / INDEL in MS Excel format
Alternative Splicing Patterns in MS Excel format
Fusion Gene File in MS Excel format
Novel Exon File in MS Excel format
Others (open for discussion)

RNA-Seq (miRNA)

Alignment Files in BAM format (known miRNA)
Alignment Files in BAM format (to other known RNAs, i.e. snRNA, snoRNA and etc.)
miRNA Expression Level File in MS Excel format
*List of Differentially Expressed miRNA in MS Excel format

*Includes 1 pairwise comparison for every 2 samples submitted for sequencing.  Additional comparisons are welcome, please contact us for details.

Target Prediction of miRNA
Novel miRNA File in MS Excel format
Expression level of other known RNAs
Others (open for discussion)

ChIP-Seq

Alignment Files in BAM format
List of Peaks in Excel format
List of Annotated Peaks in Excel format
BigWig File For Peaks Visualisation in Integrative Genomics Viewer (IGV)

Others (open for discussion)

Human Exome Sequencing

Alignment Files in BAM format
SNP / INDEL Files in standard VCF format
List of Annotated SNP / INDEL Files in MS Excel format

*Please click here for the target file that we used for analysis.

List of Annotated somatic SNP /INDEL in MS Excel format
Annotation against PHIAL in MS Excel format
Others (open for discussion)

Bisulfite Sequencing

Alignment Files in BAM format (Human and Lambda if applicable)
List of Annotated CpG Methylation Sites in Text/Excel format
List of Annotated CHG and CHH Methylation Sites in Text format
Bisulfite conversion rate of Lambda (if applicable)

Others (open for discussion)

de novo Genome Sequencing

de novo Assembly Files (raw files and contigs) in various formats
Predicted Coding Gene Files in Text format
List of Annotated Coding Gene in Text format
List of Repeats in Text format
List of non-coding RNA in Text format

Circos Diagram for visualisation of the genome
Others (open for discussion)

de novo Transcriptome Sequencing

de novo Assembly Files (raw files and contigs) in various formats
List of Transcripts in FASTA format
List of Annotated Transcripts (GO) in Excel format
Gene / Transcript Expression Level in Excel format
*List of Differentially Expressed Gene / Transcripts in Excel format

*Includes 1 pairwise comparison for every 2 samples submitted for sequencing.  Additional comparisons are welcome, please contact us for details.

Others (open for discussion)

Metagenomics Sequencing
(Whole Genome Shotgun)

de novo Assembly Files (raw files and contigs) in various formats
BLAST files (raw) in native BLAST format
Taxonomy Tree
Species Composition in Excel format

Others (open for discussion)

Metagenomics Sequencing
(16s Amplicon)

Joined Paired-End Reads in FASTA format
OTU Table in BIOM format
*Taxonomy Summary
*Results of Alpha Diversity (diversity within sample group)
*Results of Beta Diversity (comparison of diversity between groups of sample)
*List of Differentially OTUs in Excel format

*Includes 6 between group comparisons for every project. Additional comparisons are welcome, please contact us for details.

Others (open for discussion)







Pacbio Sequencing - Specific Deliverables Based On Project Type

For analysis needs beyond our routine analysis pipeline (standard deliverables), customized assistance could be provided (custom deliverables). Please note that the list below is by no means an exhaustive list of deliverables possible. Do contact us if you cannot locate what you need. Final deliverables are subjected to mutual agreement between CGS and users.

As Pacbio Sequel system will be on board at CGS soon, data deliverables will be updated accordingly, tentatively in June 2017. Stay tuned!

Type of Project Standard Deliverables Custom Deliverables

de novo Genome Sequencing

de novo Assembly Files (raw files and contigs) in various formats
Predicted Coding Gene Files in Text format
List of Annotated Coding Gene in Text format
List of Repeats in Text format
List of non-coding RNA in Text format

Circos Diagram for visualisation of the genome
Others (open for discussion)

Long-Range Structural Variation

Alignment Files in BAM format
List of Structural Variations in Excel format

Others (open for discussion)