Data Management
Efficient and secure data management is a key part of our service. This section outlines how we handle data delivery, storage, retention, and the specific deliverables included in each service.
Delivery Method
Data is provided via the SciLifeLab Datacenter Data Delivery System (DDS).
Storage & Retention
CTG stores data on secure COSMOS-SENS servers (LUNARC, Lund University) for internal processing. Delivered data is retained for 3 months before deletion. Please backup your data, as CTG cannot recover lost or corrupted files.
Deliverables
Each delivery includes:
- FASTQ files (raw sequencing data)
- QC report (FastQC & MultiQC)
- MD5 checksum file (for data integrity verification)
We process data using the following reference genomes:
- Human: GRCh38 (Ensembl)
- Mouse: GRCm39
- Pig: Sscrofa11
- Rat: Rnor6.1
Reference details are included in the delivery.
Our workflows use open-source tools. Software versions and libraries used are documented in each delivery. The standard computational service is free of charge.
Find service-specific details below:
Only default deliverables
Optionally CRAM files containing sequences aligned to one of our available reference genomes.
We use nf-core rnaseq pipeline to process RNA libraries. Included in the result is at least a custom QC report, quantified and aligned transcripts.
10x Genomics
For all single-cell projects using 10x Genomics kits, analysis with Cell Ranger or Cell Ranger ARC is included. The analysis output will be delivered alongside the FASTQ files.
For more details on the output, refer to:
- Cell Ranger Output Overview
- Cell Ranger ARC Output Overview
Usage of reporter genes need to be specified in iLab before project start and the exact sequence information and gene co-ordinates need to be submitted to be included during sequencing read alignment.
Parse Biosciences
Data generated using Evercode can be analysed using TrailMaker.
For Spatial Gene Expression projects, CTG uses either Visium or Visium HD. The following files are included in the delivery:
- Tissue images in TIF or JPG format
- Spot pixel coordinates in JSON format
- Analysis output from Space Ranger (details here)
You can meet us, along with other bioinformaticians from NBIS at NBIS drop sessions. We are happy to take questions, but if you need more extensive bioinformatic support we recommend contacting: NBIS – National Bioinformatics Infrastructure Sweden.
Contact Information for Bioinformatics
cglu [dot] bioinformatics [at] scilifelab [dot] se (cglu[dot]bioinformatics[at]scilifelab[dot]se)
Address
BMC - Biomedical Centre D14
Klinikgatan 32
221 85 Lund
