liftover files clarification

[Johan Henriksson]

hi!

I am trying to lift regions from human<->mouse and I have found

http://hgdownload.cse.ucsc.edu/goldenPath/hg38/liftOver/hg38ToMm10.over.chain.gz

and

http://hgdownload.cse.ucsc.edu/goldenpath/hg38/vsMm10/hg38.mm10.all.chain.gz

could someone please clarify the difference as these files are fairly different? would be worth also adding a note to the FTP site

thanks!

/Johan

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Johan Henriksson, PhD
Karolinska Institutet / European Bioinformatics Institute (EMBL-EBI)
Labstory - Integrated laboratory documentation and databases (www.labstory.se)
http://mahogny.areta.org  http://www.endrov.net

[Cath Tyner]

Hi Johan,

Thanks for contacting the UCSC Genome Browser support team, and thank you for your patience while waiting for our response regarding the definitions and differences of the <db1>To<Db2>.over.chain.gz and the "vs<Db$>" <db1>.<db2>.all.chain.gz files. Below is a summary followed by additional details which explain the major differences of these files. 

Summary:

• hg38.mm10.all.chain.gz contains all chained lastz alignments of human hg38 and mouse mm10 (Mouse Chains track).
  
  
• hg38ToMm10.over.chain.gz is a filtered subset of hg38.mm10.all.chain.gz, containing only the parts of chains that are included in the single-coverage "net" (Mouse Nets track).
  
  
• The vsMm10 download directory contains chains, nets and a couple more stringently filtered versions of nets briefly described in the README.
  
  
• The liftOver download directory contains the complete set of *.over.chain.gz (i.e. net-filtered chains) from hg38 to other genomes, for use with our liftOver utility or web tool.
  
  
• Viewing the Mouse Chains and Mouse Nets tracks (as seen in this session) in the Genome Browser helps to visualize the differences. Both are subtracks of the Placental Chain/Net track in the Comparative Genomics group. The chain track represents the all.chain file, and the net track represents the over.chain file. 
  

Details:

all.chain files
See the index-page README for the all.chain.gz files here:
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/vsMm10/

The lastz alignment data is described here: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/vsMm10/
In addition to chains, the all.chain file stores lastz alignment data, like this:

##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
##gapPenalties=axtChain O=400 E=30
# lastz.v1.03.66 H=2000 --format=axt+
#
# hsp_threshold      = 3000
# gapped_threshold   = 3000
# x_drop             = 910
# y_drop             = 9400
# gap_open_penalty   = 400
# gap_extend_penalty = 30
#        A    C    G    T
#   A   91 -114  -31 -123
#   C -114  100 -125  -31
#   G  -31 -125  100 -114
#   T -123  -31 -114   91
# seed=1110100110010101111 w/transition
# step=1

over.chain files
See the index-page README for over.chain files here: 
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/liftOver

Here are a few lines from the liftOver/hg38ToMm10.over.chain.gz file.
The over.chain file contains one line for each alignment chain, followed by multiple lines describing the alignment gaps within that chain.
Chain format: http://genome.ucsc.edu/goldenPath/help/chain.html

chain score tName tSize tStrand tStart tEnd qName qSize qStrand qStart qEnd id
chain 619757641 chr14 107043718 + 24687985 105865965 chr12 120129022 + 44636774 113430848 1
11    0    1
74    0    4
100    0    1
24    0    2
7    3    0
13    551    1060
13    2    0
13    1    0
11    0    1

Resources:

• Chain format
  http://genome.ucsc.edu/goldenPath/help/chain.html

• Net format
  http://genome.ucsc.edu/goldenPath/help/net.html

• axt Alignment Format
  https://genome.ucsc.edu/goldenPath/help/axt.html

• LiftOver "How to" 
  http://genomewiki.ucsc.edu/index.php/LiftOver_Howto

• Syntenic Net/Reciprocal Best page
  http://genomewiki.ucsc.edu/index.php/HowTo:_Syntenic_Net_or_Reciprocal_Best

• Wiki: Chains/Nets
  http://genomewiki.ucsc.edu/index.php/Chains_Nets.

Please respond to this list if you have further questions!

Thank you for contacting the UCSC Genome Browser support team. 

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​Enjoy,​

Cath
. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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