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.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
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.
Latest Articles
Collapse
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
-
by seqadmin
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
59 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
57 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
52 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
56 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment