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Trinity RAM issue starbug16 Bioinformatics 8 02-12-2014 09:13 AM
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Old 08-12-2014, 11:19 AM   #1
sckinta
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Location: United States

Join Date: Aug 2014
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Question RAM limitation on trinity using DIAG computational resource

Hi,

Any one used DIAG grid resource to run trinity? I am wondering what is maximum RAM request in grid.

Since trinity recommends to combine all your samples from different conditions and construct only one transcriptome for expression analysis, I want to combine my 36 samples (each sample can be 50M to 100M) reads. It seems I need 4TB RAM if I followed 1GB per 1M reads standard.

Also, I am wondering whether normalization will compromise the assembly quality a lot or not, especially considering that I want to detect low expressed factors.

Thank you

Last edited by sckinta; 08-12-2014 at 11:23 AM.
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Old 12-19-2014, 11:38 AM   #2
jevcampe
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Hi,

May I ask how you managed to run trinity. Did you run it on DIAG?

Cheers
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