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-SeqChIP-SeqATAC-Seq
Required from the usersSample 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
ProcessesDemultiplexing;
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 filesRaw 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 noteOnly up to 4 comparisons for differential expression analysis.

Basic bioinformatics analyses single cell sequencing (10x Genomics)

 scRNAseqscVDJseqscCITEseqscATACseq
Required from the usersApplied 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
ProcessesDemultiplexing
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 filessummary 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.

CategoryServiceDetails
Whole Genome Solutionsde novo genome assemblyDe novo genome assemblies assume no prior knowledge of the source DNA sequence length, layout or composition.
Variant (SNP & INDEL) discoveryVariant calling entails identifying single nucleotide polymorphisms (SNPs) and small insertions and deletion (indels) from NGS data.
Structural variant discoveryAnalysis on the large genomic variants such as deletions, duplications, insertions, inversions, and translocations. One typical case is copy number variations (CNVs).
Expression analysisCustomized differential gene expression analysisThis 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 analysisAnalysis of the various isoforms on expression level among the samples.
de novo transcript assemblyDetect the unannotated transcripts from the expression data.
Small RNA expression analysisProfiling the small RNAs from miRNA-Seq.
Novel isoform identificationDetect the unannotated isoforms in the expression NGS datasets.
EpigeneticsTranscription factor binding sites predictionPredict potential TFBS in the given target genomic regions by the public database.
Peak Analysis for ChIP-Seq projectsFurther study on the peaks by motif analysis, the association of genes from different biotypes, or the interaction with other genomic elements.
DNA methylationDifferential methylation analysisIdentify the differentially altered CpG sites in the experiments.
VisualizationCustomized figuresWe 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 analysisGene ontology (GO) analysisGO 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).
PublicationAdditional analysis for revision.This is for the clients who received customized service and now need additional analysis for revision.
GEO uploadUpload 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.