A shot in the dark, the conservation track tells you how the specific gene segment or stretch of DNA was conserved among the different species in questions.
So, if galgal3 has a conservation track, you should simple be able to
liftOver that and use it for your purposes, until new homology/convervation analysis is done.
Liftover of conservation track (mutli7z) from galgal3 to galgal4
multi7z This track shows a measure of evolutionary conservation in 7
vertebrates, including bird, mammalian, amphibian, and fish species,
based on a phylogenetic hidden Markov model, phastCons (Siepel et al.,
2005). Multiz alignments of the following assemblies were used to
generate this track:
chicken (May 2006 (WUGSC 2.1/galGal3), galGal3) human (Mar 2006, hg18)
mouse (Feb 2006, mm8) rat (Nov 2004, rn4) opossum (Jan 2006, monDom4)
X. tropicalis (Aug 2005, xenTro2) zebrafish (Mar 2006, danRer4)
Download the multi7z track from galgal3 ucscftp
Gunzip and convert it to bed,
gunzip -c multiz7way.txt.gz | cut -f2-7 > multiz7way.bed
Download the liftOver chain file,
Download the liftOver utility for your system architecture,
liftOver multiz7way.bed galGal3ToGalGal4.over.chain.gz multiz7way_mapped.bed multiz7way_unmapped.bed
multiz7way_mapped.bed is your file, convert it to bedGraph (coverage file) or bam/wig/bigwig, whatever you like and upload as a custom track to ucsc.
Please confirm the efficacy of this answer, before using it in downstream research.
But how do I get the conserved coordinates and liftover to galgal4? Is it possible to use multiz alignment to align the genomes you wnat yourself?
Thanks a lot!!
I updated my answer.
Thanks a lot Sukhdeep for writing step-by-step instructions. It was very useful!!
Hi Sukhdeep, Thanks a lot for your answer. Im confused as to what the different columns are. The 2nd, 3rd and 4th columns are coordinates in mutiz7way.txt.gz. What are 5th, 6th and 7th columns? Which column is the conservation score? and how do I retain the conservation score after liftOver to Galgal4. Is that possible? because I notice after liftOver the last column becomes zeroes throughout. Thanks a lot!!!
For second question,