The Genomic Facility in IZKF provides various of bioinformatic analyses under two main categories: basic analysis and advanced analysis. The basic analysis is included in each run of microarray and NGS experiment, but the advanced analysis is launched by consult meeting.
Basic analysis
The basic analysis provides the standard procedure without too much customization. Anything beyond the standard pipeline should be considered as advanced analysis with additional charge and collaboration. If you only require FASTQ files without any further analysis, please also let us know.
Below are the tables showing the analyses included in the basic analysis for bulk sequencing, microarray (Affymetrix) and single cell (10x Genomics) sequencing:
Basic bioinformatics analyses for bulk sequencing and microarray
| RNA-Seq | ChIP-Seq | ATAC-Seq | |
|---|---|---|---|
| Required from the users | Sample sheet with proper sample names; Brief description of the experimental design; Preferred genome assembly | Sample sheet with proper sample names; Brief description of the experimental design; Preferred genome assembly | Sample sheet with proper sample names; Brief description of the experimental design; Preferred genome assembly |
| Processes | Demultiplexing; Quality check; Trimming; Alignment; Normalization; Differential expression analysis if replicates are included and experimental design is clear. | Demultiplexing; Quality check; Trimming; Alignment; Normalization; Peak calling if experimental design is clear. | Demultiplexing; Quality check; Trimming; Alignment; Normalization; Peak calling if experimental design is clear. |
| Result files | Raw data (BCL), FASTQ, BAM, BigWig, count tables, IGV session, QC report; PDF report | Raw data (BCL), FASTQ, BAM, BigWig, BED for peaks, IGV session, QC report; PDF report | Raw data (BCL), FASTQ, BAM, BigWig, BED for peaks, IGV session, QC report; PDF report |
| Application-specific note | Only simple comparisons for differential expression analysis. Multi-factor comparison is regarded as advanced analysis. |
Basic bioinformatics analyses single cell sequencing (10x Genomics)
| scRNAseq | scVDJseq | scCITEseq | scATACseq | |
|---|---|---|---|---|
| Required from the users | Applied 10x genomics kit for library preparation Index information of the libraries | Applied 10x genomics kit for library preparation Index information of the libraries | Applied 10x genomics kit for library preparation Index information of the libraries | Applied 10x genomics kit for library preparation Index information of the libraries |
| Processes | Demultiplexing Sequencing quality check Cellranger count procedure | Demultiplexing Sequencing quality check combined analysis for sc mRNA expression and V(D)J with cellranger | Demultiplexing Sequencing quality check combined analysis for sc mRNA expressin and antibody capture libraries with cellranger | Demultiplexing Sequencing quality check scATAC analysis with cellranger |
| Result files | summary reports for the results raw data(bcl) fastq QC report for sequecing results BAM and bai files after alignment raw count matrix filtered count matrix cloupe file for browsing in Loupe Browser | summary reports for the results raw data(bcl) fastq QC report for sequecing results BAM and bai files after alignment sample count matrix cloupe file for browsing in Loupe Browser fasta, fai, annotation, bam and bai files for V(D)J consensus fasta, fai, bam and bai files for oncatenated V(D)J reference segments Annotated contigs and consensus sequences of V(D)J rearrangements fasta, fastq and annotation for contigs vloupe file for browsing in Loupe Browser | summary reports for the results raw data(bcl) fastq QC report for sequecing results BAM and bai files after alignment raw count matrix filtered count matrix cloupe file for browsing in Loupe Browser | summary reports for the results raw data(bcl) fastq QC report for sequecing results BAM and bai files after alignment peak bed file and annogtation raw peak bc matrix filtered peak bc matrix filtered tf bc matrix single cell calling cloupe file for browsing in Loupe Browser |
Advanced analysis
The advanced analysis goes according to the need of the project and our expertise in the facility. Participation in the early phase of the project is recommended. And advanced analysis requires coauthorship for future publication.
Because of our limited manpower, we list the customized services here for your reference. After knowing the exact needs, we will estimate the time we need and the relevant cost for the service. The booking of the advanced service is required so that we can work intensively together in an efficient way. During the booked period for the service, we ask for a weekly meeting to guarantee the progress of the project.
| Category | Service | Details |
|---|---|---|
| Whole Genome Solutions | de novo genome assembly | De novo genome assemblies assume no prior knowledge of the source DNA sequence length, layout or composition. |
| Variant (SNP & INDEL) discovery | Variant calling entails identifying single nucleotide polymorphisms (SNPs) and small insertions and deletion (indels) from NGS data. | |
| Structural variant discovery | Analysis on the large genomic variants such as deletions, duplications, insertions, inversions, and translocations. One typical case is copy number variations (CNVs). | |
| Expression analysis | Customized differential gene expression analysis | This service includes any comparisons, non-standard normalization needed, filtering of the genes and customized figures. |
| Characterizing the given gene sets. | Any given gene set can be characterized by its association with gene annotation, overlap with other datasets, or conservation. | |
| Splice variant expression analysis | Analysis of the various isoforms on expression level among the samples. | |
| de novo transcript assembly | Detect the unannotated transcripts from the expression data. | |
| Small RNA expression analysis | Profiling the small RNAs from miRNA-Seq. | |
| Novel isoform identification | Detect the unannotated isoforms in the expression NGS datasets. | |
| Epigenetics | Transcription factor binding sites prediction | Predict potential TFBS in the given target genomic regions by the public database. |
| Peak Analysis for ChIP-Seq projects | Further study on the peaks by motif analysis, the association of genes from different biotypes, or the interaction with other genomic elements. | |
| DNA methylation | Differential methylation analysis | Identify the differentially altered CpG sites in the experiments. |
| Visualization | Customized figures | We can do the figures according to the request of the clients and provide the scripts for reference. The clients should exact define the data and the statistics required for this service. |
| Functional analysis | Gene ontology (GO) analysis | GO analysis determines the over-representative GO terms of enriched functions or interactions. |
| Gene set enrichment analysis (GSEA) | Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). | |
| Publication | Additional analysis for revision. | This is for the clients who received customized service and now need additional analysis for revision. |
| GEO upload | Upload data to GEO. Sample overview according to GEO's standard is required from the clients. |
However, these listed services may not match your needs in your creative projects. If you have certain requests not following the standard workflow, we are still happy to discuss with you and see whether our expertise and capacity fit your need or not. Please feel free to contact us through email or contact us form.