Thread: Tophat Run time
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Old 06-21-2010, 06:29 AM   #1
Junior Member
Location: India

Join Date: Jun 2010
Posts: 5
Question Tophat Run time

Dear all,

I am currently running tophat to align human genome reference(hg19 bowtie index) to illumina pair-end data of size 17Gb each(17*2). Its almost 24 houurs and its still running. I wonder how much more time it would take to finish the process? . Concurrently i am also running Maq for 75bp single read of size 15GB with a reference size of 30mb(binary human genome file).

My system configuration is 64Gb Ram with 8 core processor(Which i feel is one among best configuration available in industry. Do i need to update my system configuration for NGS data analysis?If so please provide me the config).

And i also like to know how much processing time it would take if i run the Tophat and Maq separately?

Hopping for a speedy reply asap.

bassu is offline   Reply With Quote