iCount
iCount copied to clipboard
tomazc
Support Prokaryotic Genomes
Recently bacterial labs have started to perform iCLIP and our lab is planning to perform experiments on some bacterial strains. It will be a big enhance to support all of this community with a tool available for them.
This might be a stupid question, but... What modifications need to be done to support this?
Well, I'm not sure. I know that we can directly download lots of Eukaryotic genomes but none Prokaryotic. I assume that we could feed the pipeline with a custom bacterial gft file, although I'm not sure on the Genialis visual version. Bacterial labs cannot afford a full-time bioinformatician and probably prone to buy your product. The bacterial annotation has a single chromosome and usually several plasmids. In the other hand doesn't have introns or specify 5'- 3' UTRs. Genes usually appear as long chains of coding sequences that in occasions overlap to each other on the same or different strand. Therefore, I suppose that we couldn't use segment command either RNA maps, but wonder how it will deal with this really different annotation format...
OK, this seems like a big feature to me. It would make sense to schedule a dedicated meeting to discuss expected outcome vs. current state. Then we can decide how to approach this task and plan technical details.
No worries!! I was thinking out loud and I wrote it here... :) I believe there are more relevant things to work in. I'll give it a try as it is and we can discuss it in the future. Thanks!!