After your samples have been prepared and sequenced, you will receive a link to the BSF download portal via e-mail. The e-mail contains instructions how to set a password and how to mass-download larger sets of unaligned BAM files. If further bioinformatic data processing has been requested, we will separately provide you with aligned BAM files as well as more detailed data analysis reports.
In contrast to the FASTQ format, the BAM format utilizes an unambiguous schema to encode base quality scores, and it allows for modelling of metadata. Our metadata annotation includes instrument information, run dates, the sequence of programs that were run for raw data production and conversion, as well as version numbers and even complete command lines. The BAM format also permits annotation of adapter sequence clipping or unique molecular identifiers (UMIs) in a standardized manner. Converting from the rich BAM format to FASTQ is simple, the reverse process generally requires additional information. Amongst many tools for the conversion of (unaligned) BAM into FASTQ format, the Picard tools SamToFastq[MS1] algorithm would be an option that works well.
We tend to pool several samples into larger pools to optimize for sequencing yield by increasing the sequence complexity of both, payload reads and index reads. To reach the desired coverage, a pool may need running on more than one lane giving rise to one unaligned BAM per sample and lane. In the analysis, all BAM files for the same sample but different lanes need to be considered, otherwise data will be lost, and the read coverage will be considerably lower than expected.
Your sequencing data will be accessible via the BSF data download portal on a secure web server. Please ensure that you have downloaded and backed up all your data within 90 days. While the BSF archives the raw data in longer-term storage, we cannot guarantee successful data retrieval over longer time periods. Even if the raw data can be successfully recovered at a later point in time, data retrieval and re-processing can be time consuming and may lead to project delays in the future.
For all publications arising from collaborative academic sequencing, the BSF should be acknowledged through a sentence in the Acknowledgements section (“Next-generation sequencing (and data analysis) was performed by the Biomedical Sequencing Facility at CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences.”) or through co-authorship, depending on the scope and scale of the BSF’s contribution. Please inform us when you are preparing a manuscript that falls into this category, and we are happy to provide paragraphs for the Methods section and assist with data upload into the relevant public repositories.
The Biomedical Sequencing Facility is an academic technology platform aiming to serve life science researchers and clinicians with state of the art next-generation sequencing technologies. We handle patient material in the context of larger studies that require an application for ethical consent. We can thus not serve individual consumers with such requests but the Humangenom Austria at the Medical University Innsbruck is preparing a larger study to determine whole genome sequences of blood donors living in Austria. This project will contribute towards the Genome of Europe project.
By Austrian law, genetic counselling is limited to medical specialists for human genetics only. Please do not send any medical records or other personally identifiable material. The following organisations provide genetic counselling in Austria:
Humangenetik Medical University Graz
Humangenetik Medical University Innsbruck
Humangenetik Medical University Wien
