It”s often a good idea (especially for large datasets) to use a subset of the reads for some preliminary analyses. A smaller dataset can be useful for figuring out the alignment parameters or checking for alignment problems.
Year: 2013
Introducing the Omixon Academy!
It’s a great pleasure to present you the Omixon Academy, a series of detailed blog entries and tutorials about bioinformatics and next-generation sequencing. We have been creating such guides for weeks and have received amazing feedback about that.
Bioinformatics for Beginners – The UCSC Genome Browser
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.
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 <span class="meta-nav">→</span>