Analyzing & Visualizing NextGen Reads with Magic-BLAST

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.

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

This link goes to an interactive version of the notebook presented in the workshop. Please Note:  that it may take up to 10 minutes to load the first time you access these materials.