bowtie2 error - RAM

[kiara_bioinfo]

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

[GenoMax]

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.

[kiara_bioinfo]

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!

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.

[GenoMax]

You can split your sequence file and map in batches.

[kiara_bioinfo]

No luck!, still same error! I guess the index is too large for my PC to run it through!

[GenoMax]

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?