View source for Minimal Steps For LiftOver

This doc is a stripped down version of /kent/src/hg/doc/liftOver.txt.

The following describes the minimal steps needed to create a liftOver chain file  that converts annotations between bacterial genome builds (genome size ~4Mb).

[1] Split the query (NEW) genome build by FASTA record using faSplit:

<code><pre>$ faSplit sequence NEW.build 2 chr</pre></code>

'''NOTES''': There are 2 fasta records in the NEW build, therefore, I used the argument '2' to split the build into two files. Each file contains one FASTA record, chr0 and chr1. Also need to create .lft files (for step [3]) that describe the two sequences.  If breaking the sequences into chunks using the 'size' parameter, just use the -lift option.  Otherwise, need to make your own .lft files. For example, chr0.lft contains:

<code><pre>
0       chr 3061531 chr      3061531
</pre>
</code>
where columns are:
<code><pre>
start seq_name size seq_name size
</pre></code>

Setp [6] requires chrom.sizes files that contain the sequence lengths of the FASTA records in the builds:

<code>
<pre>
$ cd path_to_OLD_build
$ twoBitInfo OLD.2bit chrom.sizes
$ cd path_to_NEW_build
$ twoBitInfo NEW.2bit chrom.sizes
</pre>
</code>

[2] BLAT query sequences from [1] against the OLD build:

<code><pre>
$ blat path_to_OLD_build/OLD.2bit path_to_NEW_build/chr0.fa OLD.chr0.psl -tileSize=12 -minScore=100 -minIdentity=98 -fastMap
$ blat path_to_OLD_build/OLD.2bit path_to_NEW_build/chr1.fa OLD.chr1.psl -tileSize=12 -minScore=100 -minIdentity=98 -fastMap
</pre></code>

'''NOTES:''' Not using ooc file becuase genome build is small.  Probably a good idea to use a ooc file for larger genomes i.e. > X(?) Mb.

[3] Use liftUp to change the coordinate system.  Requires .lft files created in step [1]:

<code><pre>
$ liftUp -pslQ chr1.psl chr1.lft warn OLD.chr1.psl 
$ liftUp -pslQ chr0.psl chr0.lft warn OLD.chr0.psl 
</pre></code>

[4] Chain together alignments from [3] using axtChain:

<code><pre>
$ axtChain -linearGap=medium -psl chr0.psl path_to_OLD_build/OLD.2bit path_to_NEW_build/NEW.2bit chr0.chain
$ axtChain -linearGap=medium -psl chr1.psl path_to_OLD_build/OLD.2bit path_to_NEW_build/NEW.2bit chr1.chain
</pre></code>

'''NOTES''': Note the -psl argument.  This allows axtChain to accept psl as input.  I haven't tested this using blastz instead of BLAT.  I figure you can convert the lav output from blastz using lavToAxt then use axtChain, ignoring the -psl option.

[5] Combine and sort chain files from [4]:
<code><pre>
$ chainMergeSort *.chain | chainSplit chain stdin
</pre></code>
'''NOTES''': This creates a directory 'chain' whicn contains a chr.chain file.  The OLD build use here only contained one chromosome.  Not sure if axtChain will create one chain file for each target chromosome.

[6] Make alignment nets from chains in [5]:
<code><pre>
$ cd chain
$ mkdir ../net
$ chainNet chr.chain path_to_OLD_build/chrom.sizes path_to_NEW_build/chrom.sizes $ ../net/chr.net /dev/null
</pre></code>
'''NOTES''': This step requires the chrom.sizes files from step [1].

[7] Create liftOver chain file:

<code><pre>
$ netChainSubset ../net/chr.net chr.chain ../over/chr.chain
</pre></code>

[8] Use your new liftOver chain file:

<code><pre>
$ liftOver to_be_converted.bed ../over/chr.chain conversions.bed unmapped
</pre></code>