provide support for conservation score tracks

[nathandunn]

http://genome.ucsc.edu/FAQ/FAQdownloads.html#download19 -> http://hgdownload.cse.ucsc.edu/downloads.html#human -> http://hgdownload.cse.ucsc.edu/goldenPath/hg38/vsMm10/

Data explanation at the top of the last file looks like we would need minimially blastz alignments.

• hg38.mm10.all.chain.gz: chained blastz alignments. The chain format is described in http://genome.ucsc.edu/goldenPath/help/chain.html .

  • hg38.mm10.net.gz: "net" file that describes rearrangements between the species and the best Mouse match to any part of the Human genome. The net format is described in http://genome.ucsc.edu/goldenPath/help/net.html .

  • hg38.mm10.net.axt.gz: chained and netted alignments, i.e. the best chains in the Human genome, with gaps in the best chains filled in by next-best chains where possible. The axt format is described in http://genome.ucsc.edu/goldenPath/help/axt.html .

  • hg38.mm10.synNet.maf.gz: filtered net file for syntenic alignments only, in MAF format, see also, description of MAF format: http://genome.ucsc.edu/FAQ/FAQformat.html#format5

  • hg38.mm10.syn.net.gz - filtered net file for syntenic alignments only

[cmdcolin]

I had done some testing with visualizing the MAF format here https://github.com/cmdcolin/mafviewer

It seemed useful in that case to have a preprocessing step to convert the MAF into a BED type format that can be tabix indexed for BEDTabix

Would be cool to get the other formats too

[cmdcolin]

For a coarse overview of conservation score, you can just use phastCons or phyloP which are just a bigwig

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/phyloP100way/ http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons100way/

just mentioning because the title mentions conservation score. the raw files like chains and stuff are more raw. still useful in things like dotplots for example