Tweet
My computer has dual hard drives, one SSD and one traditional spinning HDD. Will keeping any of the files used in Bowtie or Tophat alignments on the SSD instead of the HDD speed up the process? Eg. The index files, input sequence reads, output files, or (in the case of Tophat) temp files. Other specs are i7-2720QM (2.2-3.3GHz), 16GB RAM. I'm thinking the bottleneck is probably the CPU since the threads almost always run at nearly 100% but thought I would ask.
-
Last edited by biznatch; 11-16-2011, 09:33 PM. -
An SSD won't help for this type of analysis. Bowtie maps the genome indices into memory, so once it's loaded the only activity from the disk should be writing out results files.
As you've seen the limitation is CPU. Bowtie allows you to spread your CPU load over many cores using the -p parameter and performance increases linearly with number of CPUs up to at least 8 cores in our tests. Tophat can also take advantage of this, but some parts of the code (calculating putative splice sites) are not multi-threaded, so will only use a single CPU. -
Thanks for the reply, I figured as much. I use 6-8 cores depending on if I need the computer for anything else while the alignments are running.Comment
-
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM -
Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM -
Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...07-08-2026, 05:17 AM
Comment