Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting

[jennaj]

Hi @YONG_JIA

@YONG_JIA

Sorry to bother you again, regarding the reference genome preparation, you have been suggesting doing the four basic indexing first and then tool-specific indexing, what is the reason for doing this? Can I just go straight to the tool-specific indexing such as the RNA-star, HISAT indexers?

If you haven’t created the SAMtools, Picard, and 2bit indexes, problems with tools can come up.

@YONG_JIA

I wonder whether you would be able to help with another problem. I got an error " java.lang.OutOfMemoryError" during the Picard indexing. I found the exact same issue was posted earlier here by someone else in github:

That error you reference is for when using Picard tools line command. For your indexing with a Data Manager in Galaxy, this same error likely means that your local Galaxy does not have enough memory to index the genome. If you are trying to index wheat from most public sources, there will never be enough memory (the genome is simply too large). Using the PLAZA version can help reduce the amount of memory needed due to the way it was reorganized, but it will still be substantial.

Related Q&A

java.lang.OutOfMemoryError, Mark Duplicates in Picard indexer builder

I encountered the same error as described in the link below: This is a closed topic in github. The answer provided in github is not clear to me, could anyone explain to me how to solve the problem in details? Thanks in advance.