Data Deliverables
Bioinformatics Core
Typical Deliverables
Depending on the sequencing technology, project type and amount of bioinformatics support required, the deliverables will differ. In general this includes:
- Sequencing Report (MS Word file) – a written report documenting the performance of the sequencing job.
- 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.
- 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).
- 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 NovaSeq / 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 CPOS 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) - PCA plot in HTML format (at least 2 samples) *Includes 1 pairwise comparison for every sample 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 sample 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) *Includes 1 pairwise comparison for every sample submitted for sequencing. Additional comparisons are welcome, please contact us for details. | - 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) |
| Human Whole Genome Sequencing | - Alignment Files in BAM format - SNP / INDEL / CNV / SV Files in standard VCF format - List of Annotated SNP / INDEL / CNV / SV Files in MS Excel format *Analysis will be conducted using DRAGEN platform. *For somatic CNV calling, a matched normal sample is required. Please contact us for further details. | - 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 - 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 sample 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 CPOS and users.
| 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) |
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