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alexdobin / STAR

RNA-seq aligner
MIT License
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Reduce time to load large genomes #441

Closed sagnikbanerjee15 closed 6 years ago

sagnikbanerjee15 commented 6 years ago

Hello,

I am using STAR to align several different libraries (at least 6). All the libraries are being mapped to the same genome hence the STAR index is same. Based on a cursory analysis I found that the time required to load the genome is around 3 minutes. There are several short contigs in the genome. I was wondering if there is any method to keep the genome loaded in the memory from the previous run so that I can eliminate the need to load the same genome for subsequent runs.

I can also map all the reads from different libraries to the same genome but the result needs to be put into different files.

Thank you.

alexdobin commented 6 years ago

Hi Sagnik,

there is a way to load the genome into shared memory and keep it there: use --genomeLoad LoadAndKeep for all the jobs mapping to the same genome (i.e. the same --genomeDir). After you are done, remove genome from shared memory with $ STAR --genomeLoad Remove --genomeDir ...

Cheers Alex

sagnikbanerjee15 commented 6 years ago

Thank you very much. Sagnik Banerjee Graduate Research Assistant Bioinformatics and Computational Biology Department of Plant Pathology and Microbiology Dr. Roger Wise's Lab Iowa State University

*"The moment I have realized God sitting in the temple of every human body, the moment I stand in reverence before every human being and see God in him

ᐧ

On Fri, Jun 22, 2018 at 3:29 PM alexdobin notifications@github.com wrote:

Hi Sagnik,

there is a way to load the genome into shared memory and keep it there: use --genomeLoad LoadAndKeep for all the jobs mapping to the same genome (i.e. the same --genomeDir). After you are done, remove genome from shared memory with $ STAR --genomeLoad Remove --genomeDir ...

Cheers Alex

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