DNA
We offer short read mapping against a reference genome and bigwig/bedgraph generation using aligners such as bwa and bowtie. Reference genome and aligners will be of your choice and we will recommend a pipeline based on the type of samples you have sequenced with us (such as WGS, exome, ChiP and other targeted approaches).
RNA
We offer short read mapping against a reference genome/transcriptome of your choice and counting of reads mapped to a feature (such as gene, exon, miRNA) of choice. Our preferred choice of aligner is HISAT2 but we are happy to accommodate any aligner of your choice. You will receive raw read counts as part of the service based on the type of samples you have sequenced with us (such as Total RNA, mRNA, microRNA and other approaches).
16S amplicon
We offer 16S analyses using QIIME2 and MOTHUR pipelines tailored specifically to the region that we target in our new service.
10X Genomics single-cell libraries
We can run 10X Genomics' Cell Ranger pipeline on gene expression, immune profiling and ATAC-seq data, with the standard reference genomes provided by 10X Genomics (for human and mouse). The outputs of the gene expression pipeline include feature-barcode matrices, Loupe files and BAM files. Link to 10X's website for a list of outputs.
10X Genomics Visium spatial gene expression
We offer to run the Space Ranger pipeline on data from spatial gene expression (Visium) libraries. The spaceranger count pipeline aligns the microscope brightfield image and the gene expression data. The outputs include a Loupe file that can be opened in 10X's software, a feature-barcode matrix, and aligned reads in BAM format. Link to 10X's website for a list of outputs.
Cost of alignment service or 10X analysis service (excluding MVA)
| lanes per run | per run (NOK) | per lane (NOK) | |
|---|---|---|---|
| MiSeq | 1 | 1,000 | 1,000 |
| MiSeq i100 | 1 | 1,000 | 1,000 |
| NextSeq | 1 | 1,000 | 1,000 |
| NovaSeq X 1.5B | 2 | 4,000 | 2,000 |
| NovaSeq X 10B | 8 | 20,000 | 2,500 |
| NovaSeq X 25B | 8 | 32,000 | 5,000 |
16S analysis: QIIME2 and MOTHUR analyses cost 1000 NOK per MiSeq run.
Do get in touch with us if you wish to use these services at post@sequencing.uio.no
Further analyses
We can offer further analyses specific to your projects on a collaborative basis. If you are interested, please get in touch.
Bioinformatic services request form
Bioinformatic services request form - to provide the NSC with information regarding bioinformatic services that you have requested.
Data delivery
- Non-sensitive data
- Sensitive data (Human patients)
- Collect the data in person using your own hard drive
- Collect the data in person after purchasing a hard drive from us
Data formats
Guide to download data from NIRD: help with NIRD
Guide to extracting data from archive (TAR) with md5 check: help with TAR
NovaSeq: Sequence data - FASTQ
NextSeq: Sequence data - FASTQ
MiSeq: Sequence data - FASTQ
Illumina data: Quality control
Obsolete: Illumina sequence data delivery (before 15th August 2011) and quality control
Data security
If this sequence data relates to human samples, you are responsible for storing it in a way that complies with the local jurisdiction.
Data storage policy (updated on Jan 1, 2025)
Data will be stored at our local storage facility for a period of 3 months from the date of the delivery mail after which it will be permanently deleted. No reminder notice will be sent before deletion.