Memory Requirements For Running Bowtie2 Tophat2 And Cufflinks
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.
• 6,149 views
•
link
written
by
ancient_learner
0 answers
No answers yet.
Log in to answer this question.
More posts like this
25M reads : paired-end ? length ?
single-end; 76bps length
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?
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