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Old 10-13-2014, 04:54 AM   #1
kiara_bioinfo
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Cool bowtie2 error - RAM

Hi all

I was trying to map a fastQ file to the hg19, using a prebuild index with Bowtie2.

But the error said there isnt enough memory.

I understand that clearly. I am quite new to bioinformatics, and I have a very silly Qn now, how much RAm is minimum needed while mapping to hg19, considering I have a large fastQ read file too???

Thanks,

Kiara
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Old 10-13-2014, 05:04 AM   #2
GenoMax
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How much RAM do you have?

bowtie2 indexes themselves need 3.2G but if you have a very large dataset then you may realistically need 16G or more.
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Old 10-13-2014, 05:06 AM   #3
kiara_bioinfo
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Unhappy

Ohoh!... I have just 8GB RAM ....

So does it mean I cannot map to a hg19 with this RAM???



//high time to change / upgrade gadgets!


Quote:
Originally Posted by GenoMax View Post
How much RAM do you have?

bowtie2 indexes themselves need 3.2G but if you have a very large dataset then you may realistically need 16G or more.
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Old 10-13-2014, 05:17 AM   #4
GenoMax
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You can split your sequence file and map in batches.
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Old 10-13-2014, 07:42 AM   #5
kiara_bioinfo
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No luck!, still same error! I guess the index is too large for my PC to run it through!
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Old 10-13-2014, 07:54 AM   #6
GenoMax
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Can you post the exact error? Also tell us how big is your sequence file(s). Are you doing the alignments in a virtual machine by chance?
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