Hi Scott,

Sorry to hear that you are having trouble. These are exact match hits to both? Contamination isn't out of the question with public databases, but I would start with filtering results first to see if that helps. If you still have concerns, a test versus the line-command version is the definitive answer.

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 could 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. Thanks!

Galaxy team

On 4/8/14 10:26 AM, Scott Tighe wrote:

Not in the case of Megablast. So sounds like there is no PhiX filter. Also I noticed that when I selected megablast, all the reads went to Bovine, but when I hand selected from galaxy a bunch of the sequences, that blasted (using NR) to Pseudomonas and other bacteria which is correct. I think your Megablast is not working properly.


Scott Tighe
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
802-656-2482 (AGTC)

On 4/8/2014 10:23 AM, Jennifer Jackson wrote:
Hi Scott,

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 it behind, control should fall out during mapping against the sample's target genome (if available).


Galaxy team

On 4/4/14 12:33 PM, Scott Tighe wrote:
Dear Team Galaxy

Is there a simple way to filter PhiX control from a sample set?


Jennifer Hillman-Jackson

The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


To search Galaxy mailing lists use the unified search at:


Reply via email to