TopHat approximate run time & memory usage?

[xinchen]

Hi everyone,

I'm using TopHat to map my RNA-seq reads to splice junctions for use in Cufflinks, but it's been taking a bit longer than I expected. One sample I ran (as an initial test) has been going for ~34 hours, and the tophat_out folder is using up around 76 GB of space. By looking in the logs, it seems to be on the "segment_juncs" step.

Each of the individual samples I hope to align have roughly 90 million reads (@ 50 nt) over 3 lanes, and I'm aligning to the human genome (hg19).

Would anyone know how long I should expect the program to run for, and also how much disk space it'll need per sample?

Thanks!

edit: I'm using single-end reads

[shurjo]

It routinely takes ~40 hours for me (~45 million reads, with - p 4 to use four threads and 16G RAM). It will delete the huge temp files it generates, so the disk usage may not be that much of any issue.

[sphil]

I'm not sure but i think that TopHat need for 75million reads about 3 Days...

[xinchen]

Thanks! It ended up taking ~50 hours for my test sample, which isn't too long

[ymc]

How can you guys compare run time and memory usage without stating the CPU and RAM you are using???