Hi all,
I am having trouble with running Cufflinks on PE RNA-Seq libraries generated from HiSeq machine. I have used Tophat to successfully mapped those PE reads (about 160 millions reads), which gave me a BAM file about 6GB for each library. Then I fed the BAM file to Cufflinks running with 20 cores. Now the problem is it seems Cufflinks is taking more than 120GB ram, and is taking very long (about a week) to run one library. Have any of you had similar experience? Am I doing something wrong? Any suggestions? Thanks!
I am having trouble with running Cufflinks on PE RNA-Seq libraries generated from HiSeq machine. I have used Tophat to successfully mapped those PE reads (about 160 millions reads), which gave me a BAM file about 6GB for each library. Then I fed the BAM file to Cufflinks running with 20 cores. Now the problem is it seems Cufflinks is taking more than 120GB ram, and is taking very long (about a week) to run one library. Have any of you had similar experience? Am I doing something wrong? Any suggestions? Thanks!
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