We had a great turnout for the 2019 Student Research Symposium as usual, with everyone in the lab either presenting their work or judging the work of others. Congratulations to Dean’s award for Science winners Holly Norman and Ashelyn Lutrick for their presentation on “Analyzing the Presence, in Humans, of crAssphage: A Highly Abundant Bacteriophage Found Around the Globe”.
Here are Jillian, Melisssa, Shane, and Rob in front of Jillian and Shane’s posters.
Our new service, searchSRA provides you with hundreds of bam-format files. However, running the search is only part of the battle, and the next daunting step is the downstream processing. Here are some hints about processing the data.
AKA: how to remove contamination from your metagenome! We use sharks genomes, but it works with humans, corals, and other things too!
A while ago we wrote deconseq to allow you to remove contamination from your sequence libraries. We used an HTS-mapper to map the reads in your sequences to your reference genome, and then filtered the sequences after mapping.
This is trivial to do with modern sequence analysis tools, and so we provide recipes here for filtering your reads based on matches to a reference genome. Read more to find out how!
The NCBI SRA contains a lot of data – about 1016 bp at the moment! However, searching that has always been problematic. We’re happy to unveil a new search SRA service that allows you to search the random metagenomes in the SRA using either DNA or protein queries.