Analyzing & Visualizing NextGen Reads with Magic-BLAST
Workshop Duration: 2 hours
Content Difficulty: Intermediate
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
Data Access Technology: Jupyter Notebook, Command-line, Web
NCBI Resources: EDirect, SRA, MagicBLAST, Genome Data Viewer (GDV), Sequence Viewer
Last Reviewed: November 2, 2022