Using RepeatModeler for novel assembled genome

Question

[nehleen11]

I am working for genome assembly and annotation. Recently the assembly has been completed to scaffolds and my next target is to find the Repeat regions in my assembled genome using this scaffolds. from literature review I have chosen RepeatModeler but totally unable to understand how to run it ? or how to interpret the results from the documentation. I am really in a need of help from the experts who have already used RepeatModeler successfully ... it would be very kind if any one can share the detailed process or what i should do for identifying denovo repeats in my assembled genome? * Assembly Level : Scaffold * comptational Power : 16 CPU, RAM : 96 GB, Storage : 1TB ** PLEASE REQUIRE ADVISE FROM PEOPLE WHO HAS USED REPEAT MODELER

[WouterDeCoster]

Hi nehleen11,

Your question is not more urgent than any other question here and writing Urgent will not get you any help faster.

However, what will get you faster help is:

• use tags appropriately: as such experts can easily find your question. In this case "repeatmodeler" would have been a very logic tag. I have added this for you.
• provide a link to the tool you are talking about: don't make us search for it
• tell us what you tried, including the exact commands. It would be easier to point out what went wrong
• use a more specific title. I have also adapted this for you.

Welcome to biostars. Interesting guidelines for posting can be found in the following posts:

• How To Ask Good Questions On Technical And Scientific Forums
• How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
• How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking

Cheers,
Wouter