Learn more about JGI’s PhycoCosm data portal, an interactive collection of sequenced algal genomes, omics data and comparative analysis tools.
Reference: A One-Stop Shop for Analyzing Algal Genomes
Questions and Answers
1. Q(uestion): Why would your Tree ever differ from NCBI Taxonomy?
A(nswer): If you find that our trees are incorrect or need to be changed, please contact us and we’ll work work it out
2. Q(uestion): Do you publish the data sets the trees are based upon?
A: This is still work in progress as new genomes are being added. We do plan to publish the tree or their parts and data it is based on
3. Q(uestion): Can you please explain again how did you pick genomes to be on the genomes portal? For the taxa I work on, there are 7 genomes on NCBI but your portal has only 2 of them.
A: Watch the video (above) for the answer provided by Sara
4. Q(uestion): Are all CSP produced data automatically assembled and run through your annotation pipeline then added to PhycoCosm (if relevant)?
A: For every genome that we sequence, we provide full analysis (assemble, annotate, work on initial analysis) and share data in PhycoCosm.
For genomes not sequenced by JGI, if PIs are interested are working with us please contact me at ivgrigoriev@lbl.gov
5. Q: If we have RNAseq or proteome data that is based on a model that is not based on a genome model with PhycoCosm, how do we go about getting it in your system?
A: I think the best way is to contact us for multiomics visualization as we want to support you in getting these data on our system. If it’s not based on the gene model, that should be ok generally. We can work with you to re-map the data. If your rna-seq data doesn’t necessarily agree, we also have a way to do manual annotation – not covered in these tutorials
6. Q: On the genome synteny page, would it be possible to add a feature to look for synteny of the target genome with itself, to identify regions that might be duplicated?
A: Yes, we do routinely calculate self-alignments, usually in the dropdown of available targets on the synteny page.
7. Q: What is success rate for CSP? What makes a successful CSP?
A: Reminder: two calls for proposals are open right now – large scale CSP and FICUS with March 24 and March 17 deadlines. 25-30% of proposals are selected, pretty high in comparison to other funding agencies. The JGI doesn’t fund research; we provide the resources for free.
8. Q: What makes a successful project?
A: Combination of:
- DOE mission relevance
- Science
- User community – trying to produce resources for large groups of people. Talk to collaborators and colleagues
9. Q: Only algal genomes in PhycoCosm?
A: PhycoCosm is devoted to algae (photosynthetic eukaryotes not including plants), so populated by algal genomes thus defined. We also have some reference plant genomes to help with comparative studies of algae and we have various protists such as oomycetes. We think they’re valuable for comparative studies (see video for Alan’s response)