Question: Memory Requirements For Running Bowtie2 Tophat2 And Cufflinks
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gravatar for ancient_learner
5.5 years ago by
India
ancient_learner610 wrote:

We are getting RNAseq data (mouse genome) soon. It was done in 2 different cell types and we have to compare and identify the differences between those two transcriptomes. In the tophat2 website the index file for mouse itself shows 14Gb. If we get >25M reads (including replicates) for each cell type how much memory i can request our common server facility? (http://cmsd.uohyd.ernet.in/) I have checked other posts as well but couldn't find the exact answer that suits.

rnaseq tophat2 cufflinks • 3.3k views
ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by ancient_learner610

25M reads : paired-end ? length ?

ADD REPLYlink written 5.5 years ago by Nicolas Rosewick7.4k

single-end; 76bps length

ADD REPLYlink written 5.5 years ago by ancient_learner610

It's hard to answer exactly. I see you have tons of Ram, so you might e.g. ask for 32Gb which is not so much and I am pretty sure will suffice. Maybe 16 will be enough as well, but what if they are not?

ADD REPLYlink written 5.5 years ago by Fabio Marroni2.1k

if i clarify them about why i need that much with valid reasons that's not a problem. i am searching for authentic source to convince. In the website i dint find any where that mentions about the memory requirements in a proper way

ADD REPLYlink written 5.5 years ago by ancient_learner610
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