Analyzing & Visualizing NextGen Reads with Magic-BLAST
The application deadline has now passed. If you are interested in this workshop, you will be able to access the materials and video recording shortly after the workshop – keep an eye on this page for the link.
Next generation sequencing (next-gen) has become the standard method for obtaining genomic and transcriptomic sequences; however analysis of the large number of short reads can be complicated and requires specialized software. NCBI has developed a variation of the BLAST algorithm, Magic-BLAST, to align next-gen reads to a reference nucleotide sequence. You can import the read alignment results from Magic-BLAST into one of NCBI’s genome browsers to visualize them alongside your choice of hundreds of other NCBI annotation tracks. Thus, without having to go through a sequence assembly step, you can quickly assess the sequence set for genetic variations and map potential gene annotations.
This workshop is designed for researchers already working with next-gen data and performing DNAseq or RNAseq experiments who use command-line tools for bioinformatic analysis.
In this workshop you will learn how to:
- access and run Magic-BLAST from the command line on reads from the NCBI SRA database, without needing to pre-download the reads.
- import aligned DNAseq data into an NCBI genome browser to look for evidence of genetic variation from the reference sequence
- import aligned RNAseq data into an NCBI genome browser to look for differences in gene expression patterns
- load relevant NCBI tracks to compare known annotations with the aligned read data
- export a URL to share your alignment view with colleagues and save an image for sharing in presentations or publications
Due to curricular and technical limits, we’ve capped the number of spots to provide the best workshop experience. If you register to apply, you will be notified of your application status 2 weeks before the scheduled event.
We recommend having access to a stable internet connection and modern web browser on a laptop or desktop computer to be able to successfully participate in the hands-on exercises.