Filtering Phix

Question: Filtering Phix

4.7 years ago by

Scott Tighe • 200 wrote:

Dear Team Galaxy Is there a simple way to filter PhiX control from a sample set? S -- 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)

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modified 4.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.7 years ago by Scott Tighe • 200

4.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 -- Jennifer Hillman-Jackson http://galaxyproject.org

ADD COMMENT • link written 4.6 years ago by Jennifer Hillman Jackson ♦ 25k

4.6 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

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

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