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califano-lab / ARACNe-AP

Network Reverse Engineering through AP inference of Mutual Information
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Would you please help me to make it faster? #10

Open huqingtao2018 opened 3 years ago

huqingtao2018 commented 3 years ago

Hi, thank you for developing the ARACNe software. I'm using it to generate single cell network for a matrix of 15,000 cells and 20,000 genes and 800 transcription factors using the following command. It took more than one week and only about 30 seeds were finished. Would you please tell me Is there anyting wrong? is there any thing I can do to make it faster? How long does it usually takes to run this kind of dataset? Thank you very much.

for i in {1..100}; do java -Xmx5G -jar /2_zhanglab/xueying/software/metaVIPER/Aracne.jar -e mouse_scRNAseq.tsv -o outputFolder1 --tfs cotf-mus-current-symbol.dat --pvalue 1E-8 --seed $i --threads 50; done

garciaaxnih commented 2 years ago

Has there been discussion on making it faster to use with single-cell data?