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