Dear Team Galaxy
Is there a simple way to filter PhiX control from a sample set?
Senior Core Laboratory Research Staff
Advanced Genome Technologies Core
NextGen Sequencing/Flow Cytometry
University of Vermont and Vermont Cancer Center
149 Beaumont ave
Health Science Research Facility 303/305
Burlington Vermont 05405
This genome is available in most mapping tools, so a positive match
could be used to identify the control. But if you just want to leave
behind, control should fall out during mapping against the sample's
target genome (if available).
Sorry to hear that you are having trouble. These are exact match hits
both? Contamination isn't out of the question with public databases,
I would start with filtering results first to see if that helps. If
still have concerns, a test versus the line-command version is the
As you may have seen on the public Galaxy instance, the Megablast tool
happens to have the ' phiX174' genome as a specific target, so you
use that. Most NGS mappers have a custom reference database option
(however not Megablast, for resource reasons) and a local/cloud Galaxy
can be configured to use any Galaxy-wrapped mapper (there are many,
check the tool shed). Combined, these provide many options.
Please send "reply-all" to keep questions on list going forward.