Thread: Tophat Run time
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Old 09-17-2013, 12:17 PM   #9
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Originally Posted by crazyhottommy View Post
I was running Tophat to map a 24G single end RNA-seq fastq to hg19 with the gtf from GENECODE
I run it in a cluster with 1 node, 8 processors, ram=3gb
it took me 45hrs to finish.....

Any way to speed it up? as a regular user of the cluster, the above setting is the max resource I can have.
Split the fastq file and use multiple nodes. If you had more RAM, you could run STAR.
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