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Analyzing & Visualizing NextGen Reads with Magic-BLAST

This workshop was offered virtually on December 13, 2022.

Workshop Duration:
2 hours

Content Difficulty: Intermediate

Target Audience:

This workshop is designed for biologists who have experience with command-line and are want to analyze their next-generation sequence data in comparison to a reference sequence with annotations.

Workshop Description:

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

Jupyter notebook button icon
Please Note: The first time you access the notebook - it may take a couple of minutes to load.

Last Reviewed: November 2, 2022