Deutsch Intern
  • Flow cell Nahaufnahme
Core Unit Systems Medicine

NGS data analysis

We offer Bioinformatics analysis solutions for high-throughput sequencing, such as RNA-Seq, Dual/Multi RNA-Seq, ChIP-Seq and single cell experiments, including scRNA-seq and ATAC.

Our standard analysis includes quality assessment, filtering and trimming of the data.

 

A properly filled out order sheet or single cell submission sheet is required, in the case of single cell experiments, information on the CMOs, ADTs, and HTOs used is essential.

RIP-seq Example Analysis

Campa AR, Smith LM, Hampton HG, et al. The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR–Cas immune systems. Nucleic Acids Research. 2021;49(16):9508-25. https://doi.org/10.1093/nar/gkab704

RNA-seq Transcriptome Analysis Example

Delgobo M, Heinrichs M, Hapke N, et al. Terminally Differentiated CD4+ T Cells Promote Myocardial Inflammaging. Front Immunol. 2021;12. https://doi.org/10.3389/fimmu.2021.584538

Analysis steps Deliverables    
Demultiplexing, Quality check,
Quality and adapter trimming,
Alignment, Normalization,
Differential gene expression analysis,
Functional enrichment analysis
Raw BCL data,
Raw FASTQ files,
QC reports, BAM files (opt),
Coverage files (opt),
Count tables,
PCA and sample distance plots,
Pairwise comparison tables and plots,
Functional enrichment tables and plots
   

Analysis steps Deliverables    
Demultiplexing,
Quality check,
Quality and adapter trimming,
Filtering of host and pathogen reads,
Alignment, Normalization,
Differential gene expression analysis,
Functional enrichment analysis
Raw BCL data,
Raw FASTQ files,
QC reports,
FastQScreen read tagging reports (opt),
BAM files (opt), Coverage files (opt),
Count tables,
PCA and sample distance plots,
Pairwise comparison tables and plots,
Functional enrichment tables and plots
   

Analysis steps Deliverables    
Demultiplexing,
Quality Check, Trimming,
Alignment, Normalization,
Peak calling
Raw BCL data,
Raw FASTQ data,
BAM files (opt),
QC report
   

Analysis steps Deliverables    
Demultiplexing,
Quality check,
Quality and adapter trimming,
De novo genome assembly,
Draft genome ordering against a reference (opt),
Taxonomic identification (opt),
Genome annotation (opt),
MLST (opt), Antibiotic resistance genes screening,
Virulence genes screening
Raw BCL data
Raw FASTQ files,
QC reports,
Interactive tormes report,
assembly, annotation,
taxanomic identification report (opt),
MLST, antibacterial and virulence genes (opt)
   

Analysis steps Deliverables    
Demultiplexing,
Quality check,
Quality and adapter trimming,
Computational deconvulation of human and mouse reads,
Alignment, Normalization,
Differential gene expression analysis,
Functional enrichment analysis
Raw BCL data,
Raw FASTQ files,
QC reports, XenofilteR report (opt),
BAM files (opt),
Coverage files (opt),
Count tables,
PCA and sample distance plots,
Pairwise comparison tables and plots,
Functional enrichment tables and plots
   

Analysis steps Deliverables    
Demultiplexing,
Quality Check,
Alignment,
Filtering,
Barcode counting,
UMI counting,
Gene Expression
Raw BCL data,
Raw FASTQ data,
QC report,
Summary reports,
BAM, bai files
Raw count matrix,
Filtered count matrix
   

Analysis steps Deliverables    
Demultiplexing,
Quality Check,
Alignment,
Sequence assembly (V(D)J),
Filtering,
Barcode counting,
UMI counting,
Gene Expression
Clonotype Calling (V(D)J)
Raw BCL data,
Raw FASTQ data,
QC report,
Summary reports,
BAM, bai files
Sample count matrix
fasta, fai, annotation,
bam and bai files (V(D)J consensus,
concatenated V(D)J reference segments),
Annotated contigs and consensus sequences of V(D)J rearrangements
fasta, fastq and annotation for contigs
   

Analysis steps Deliverables    
Demultiplexing,
Quality Check,
Alignment,
Filtering,
Barcode counting,
UMI counting,
Gene Expression
Raw BCL data,
Raw FASTQ data,
QC report,
Summary reports,
BAM, bai files,
Peak bed file and annotation,
Raw peak bc matrix,
Filtered peak bc matrix,
Filtered tf bc matrix,
Single cell calling