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!
Jen Galaxy team
On 4/8/14 10:26 AM, Scott Tighe wrote:
Jennifer
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
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).
Best,
Jen 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?
S