LiftOver Howto

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This page is an interesting historical discussion and well worth the read.

HOWEVER, please note, the UCSC tool chain commands: and can now completely perform the sequence of events in your environment with your selected genome sequences.


Creating a liftOver file is very similar to a whole-genome alignment. A liftOver file is a chain file, where for each region in the genome the alignments of the best/longest syntenic regions are used to translate features from one version of a genome to another.

With competing assemblies becoming more common, liftOver file is sometimes necessary for someone that sets up his/her own genome browser of a different assembly.

This page is based on Minimal_Steps_For_LiftOver, but is even more minimalistic.

Also see the page Whole_genome_alignment_howto and Same_species_lift_over_construction for some background on tools and terminology. From that page you will also find a link to a script.

Specifically, note the page Alignments_with_Blastz and understand the script, RunLastzChain sh.txt


  • BLAT the new genome onto the old genome
  • Sort/Chain/Merge/Split/Net


  • My genome is rather small, so I don't do any splitting or lifting steps anywhere, that makes it simpler. If you need to split your genome, see Minimal_Steps_For_LiftOver: The old genome is split in chunks and lifting file is generated. After the alignment of the chunks, the resulting chains are lifted back to the original coordinates.
  • I have repeatmasked my new genome assembly. The masked fa files are in ../ci3/rm/masked
  • The old assembly is called ci2.2bit, the new assembly is in the directory ../ci3. After repeatmasking it's in rm/masked
  • I want the alignment .psl to be in the directory psl, so I did the alignment with
 mkdir psl
 for i in ../ci3/rm/masked/*.masked; do blat ../ci2.2bit $i -tileSize=12 -fastMap -minIdentity=98 psl/`basename $i .fa.masked`.psl -noHead -minScore=100; done
  • Translate psl files to chains in the directory chain:
 mkdir chain
 for i in psl/*.psl; do axtChain -linearGap=medium -psl $i ../ci2.2bit ../ci3/ci3.2bit chain/`basename $i .psl`.chain; done
  • Merge short chains into longer ones into the directory chainMerge:
 mkdir chainMerge
 chainMergeSort chain/*.chain | chainSplit chainMerge stdin -lump=50
  • concat and sort the chains:
 cat chainMerge/*.chain > all.chain
 chainSort all.chain all.sorted.chain
  • Need info about chromosome sizes for netting:
 twoBitInfo ../ci3/ci3.2bit ci3.chromInfo
 twoBitInfo ../ci2.2bit ci2.chromInfo
  • Netting: identify alignable regions from chains:
 mkdir net
 chainNet all.sorted.chain ci2.chromInfo ci3.chromInfo net/ /dev/null
  • Finally, select the right alignable regions using the nets, creating a "liftOver" file:
 netChainSubset net/ all.chain ci2ToCi3.liftOver