Quality check, alignment to reference genome, identification of enriched regions (peak calling) are included.
- Report with sequencing statistics
- Raw data in FASTQ format
- FastQC reports
- Alignment files in BAM format
- Peak files in BED format
Additional analysis on request:
Differential accessibility analysis:
Identification and annotation (human, mouse, rat, drosophila) of differential chromatin accessibility between samples.
- Report with summary of differential accessibility analysis and plots
- Files containing differentially accessibility sites or unique peaks and breakdown of those in annotated regions: introns, exons, promoters, 1-to-5 kb upstream-TSS and intergenic regions for human, mouse, rat and drosophila.
Annotation in genomic regions:
Annotation of ATAC-Seq peaks with genomic regions: introns, exons, promoters, 1-to-5 kb upstream-TSS and intergenic regions for human, mouse, rat and drosophila.
Gene ontology terms analysis:
Enrichment analysis on gene sets. Gene Ontology terms that are overrepresented in differentially bound regions may indicate the underlying biological processes involved.
Identify biochemical pathways in which genes associated with differentially methylated regions (or individual differentially methylated CpGs) may be overrepresented.
Visualization of specific genomic regions:
Visualization of results (i.e. sequencing data, peaks) at specific genomic regions (e.g. genes, promoters) in publication-ready images (human, mouse, rat).
Generated files will be available for download during 1 month and stored for an additional period of 3 months on Diagenode’s servers. Additional long-term storage of data is available upon request. Original samples are stored at Diagenode during 12 months after project completion, but will be discarded once this time is exceeded. Return shipment of samples is available upon request.