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tomazc / iCount

iCount, protein-RNA interaction analytics
http://icount.biolab.si
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Support Prokaryotic Genomes #139

Open Faitero opened 7 years ago

Faitero commented 7 years ago

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.

JureZmrzlikar commented 7 years ago

This might be a stupid question, but... What modifications need to be done to support this?

Faitero commented 7 years ago

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...

JureZmrzlikar commented 7 years ago

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.

Faitero commented 7 years ago

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!!

JureZmrzlikar commented 7 years ago

OK. :-)