Analyzing & Visualizing NextGen Reads with Magic-BLAST
This workshop concluded on October 31, 2023. Workshop materials are available here: https://www.nlm.nih.gov/ncbi/workshops/2023-10_nextgen-reads-magicblast/workshop-details.html
Next generation sequencing (next-gen) has become the standard method for obtaining genomic and transcriptomic sequences. Analysis of the large number of reads produced by these techniques requires specialized bioinformatic tools for tasks such as sequence alignment. 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 a sequence data set for genetic variations, map potential gene annotations, and view patterns of gene expression.
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 NCBI’s Genome Data Viewer (GDV) to look for evidence of genetic variation from the reference sequence
- import aligned RNAseq data into GDV 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