The UCSC Genome Browser is developed and maintained by the Genome Bioinformatics Group at the University of California Santa Cruz. The website contains a large number of reference sequences and genome assemblies from different species. Sequences and annotation sets can be downloaded or viewed in the Genome Browser.
Month: July 2013
Flashcard Fridays – Incidental findings in genetic testing
As multi-gene NGS panels and whole exome and genome sequencing become more and more accessible, clinical diagnostic protocols based on these methods are being developed as well.
As the result of these sequencing runs doesn”t only contain information about a low number of genes or a predefined set of variants, it is highly possible, that additionally to the results we “aimed for”, some other clinically relevant information is “accidentally” discovered during the analysis.
This raises a very difficult ethical question: Should the patient be told about these incidental findings or not?
Workflow Wednesdays – Part 3. Read preprocessing – Adaptor trimming
After a few weeks long sidetrack about reference sequence manipulation, let’s get back to our reads. If you’ve read my post about read quality control results, you might remember, that I found some untrimmed adaptors on the 454 reads (SRR797242.fastq). In this post, I’ll show you a few ways to remove these adaptors from the reads. Continue reading
Bioinformatics for Beginners – File formats Part 4. – Variants and annotations
VCF
The VCF format specification is available here.
VCF (Variant Call Format) is a text file format (most likely stored in a compressed (for example gzipped) form). It contains meta-information lines, a header line and data lines containing information about a position in the genome.
Flashcard Fridays – Scitable
Scitable is an online learning tool and knowledge base run by the Nature Publishing Group. It contains information mostly about genetics and cell biology. The available material is very diverse: an extensive and ever growing list of topics is discussed at different levels. A high-school student and a researcher with a PhD can both find useful and understandable information on the site.
