Hi all, I have a fundamental problem. Actually I just want the information of rearrangement between human and mouse genome. It seems UCSC provide this info. As the link http://hgdownload.cse.ucsc.edu/goldenpath/hg38/vsMm10/ shows: 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. I took a look in details about the description page, unfortunately, I still cannot really understand, problem like, what is the 'fill' line and 'gap' line mean respectively? what the relationship between two line with one space indent? and the more important is how I can get the rearrangement information? It would be great that these confusion can get answers. Thanks very much for your attention!!
1 answer
Start here:
Read this recent paper about the database:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383971/
See these very informative biostar- posts:
Find an gene as an example of how the human is related to other primates with blast
A: Online Resources For Mouse Research
See answers to many questions about UCSC:
https://genome.ucsc.edu/FAQ/FAQformat.html
Another help page:
https://genome.ucsc.edu/goldenpath/help/hgTracksHelp.html
A very nice guide to work with human genome:
http://veda.cs.uiuc.edu/CompGen2014/labs/06_Comparative_Genomics_Ma_v1.pdf
Net-format
https://genome.ucsc.edu/goldenpath/help/net.html
Other tutorials to learn:
Youtube explanations:
https://www.youtube.com/watch?v=#DNXI-M9oQl8 Only remove # after =!
This page is for training:
https://genome.ucsc.edu/training/index.html
Another guide to listen to:
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