genome index for miRdeep*

Question

[mahfuz.290066]

Hello everybody, I am not a bio-informatician that's why i don't know how to use the command line function. but I need to analyze my small RNA seq data. I did it a little but now I want to use miRdeep* to search for the novel microRNA in my seq. However, the problem is my small RNA seq is from dog and mirdeep* requires genome index for this analysis. i will be very thankful if somebody gives me some suggestion how can I overcome my problem. I am using windows and I have no access to use Linux, Mac or Ubuntu. thanks in advance and looking for your help. mahfuz

Answer 1

[Gjain]

Things you can do:

1. Try to install ubuntu on a virtual box. You then can use mirdeep2 with its full capabilities

2. CanFam3.1 can be used in mirdeep2.. more details can be found: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0153453

I hope this might get you started.

[mahfuz.290066]

Thanks a lot Gjain for your helpful suggestion, But i don't know actually how to install ubuntu on a virtual box. is there any guide or tutorial you can suggest for me plz. Thanks a lot again

[Gjain]

I am happy to help. Please check this link to install ubuntu

[mahfuz.290066]

Thanks a lot for your kind help @ Gjan

[Gjain]

You're welcome ... happy to help