LiftOver Howto

2018 UPDATE NOTE

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

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

Discussion

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 DoChainNetBlastz.pl script.

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

Outline

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

Alignment

• 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/all.net /dev/null

• Finally, select the right alignable regions using the nets, creating a "liftOver" file:

 netChainSubset net/all.net all.chain ci2ToCi3.liftOver