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
--
Jennifer Hillman-Jackson
http://galaxyproject.org
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