Transferring genomic features on new coordinates
I think the standard way of doing this is to make a chain file, then use it to do a liftOver of the annotations:

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 &gt; 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


Run liftOver:

CrossMapy.py bed ci2ToCi3.liftOver test.hg18.bed