One nifty visualization tool is a result from a three day hackathon over at Brandeis University. The open publication and repository of source code is here (https://f1000research.com/articles/6-596/v1) and here (https://github.com/NCBI-Hackathons/rnaseqview), respectively.
Formally called an ideogram, this tool draws histograms of expression (mRNA, tRNA, ncRNA and others) along the coordinates of a chromosome. You can visualize the entire set of chromosomes or simply filter and focus on one chromosome. The later would be pretty cool looking at insertions / deletions on a more global scale, showing more deleterious gross abnormalities. Another question this tool helps provide perspective; have you ever wondered if there are any biased in sequencing reads over parts of a chromosome or even all chromosomes? This tool can easily show the data. Then, there’s a host of comparisons between samples or experiments one could develop provide perspective with this tool.
Currently, it takes a SRA accession, gets read counts directly from NCBI, grabs the proper alignment coordinates (only takes human GRCh37 and GRCh38), normalizes the reads to TPM (also provides raw counts), converts the reads to .json format which can then be imported into Ideogram.js for your viewing pleasure.
Obviously, this would be seriously cool for other organisms, I’m thinking some of our plant projects right now, but since it’s open source, anyone could update / improve upon.
Thanks @ RNA-seq Viewer Team at the NCBI-assisted Boston Genomics Hackathon