run-make-liftOver

scripts to make liftOver chain files

example is for /home/jmkidd/links/kidd-lab/genomes/Dog10K_Boxer_Tasha_1.0.KP081776.1/make-liftOver/TashaToCanFam3.1/run-make-liftOver

make Dog10K_Boxer_Tasha_1.0.KP081776.1TocanFam3.1

made new params files

old = Dog10K_Boxer_Tasha_1.0.KP081776.1 new = canFam3.1

make the dirs that are needed mkdir chunks lift blatRun psl chain chainRun chainRaw net over logs

liftName Dog10K_Boxer_Tasha_1.0.KP081776.1TocanFam3.1 oldRef /home/jmkidd/links/kidd-lab/genomes/Dog10K_Boxer_Tasha_1.0.KP081776.1/ref/Dog10K_Boxer_Tasha_1.0.KP081776.1.fa oldFai /home/jmkidd/links/kidd-lab/genomes/Dog10K_Boxer_Tasha_1.0.KP081776.1/ref/Dog10K_Boxer_Tasha_1.0.KP081776.1.fa.fai oldOOC /home/jmkidd/links/kidd-lab/genomes/Dog10K_Boxer_Tasha_1.0.KP081776.1/ref/11.ooc oldChromsDir /home/jmkidd/links/kidd-lab/genomes/Dog10K_Boxer_Tasha_1.0.KP081776.1/by-chrom/ newChromsDir canfam-by-chrom/ newFai /home/jmkidd/links/kidd-lab/genomes/canFam3.1/canFam3.1-noY/canFam3.1.fa.fai chunksDir chunks/ liftDir lift/ blatOutDir blatRun/ pslDir psl/ chainDir chain/ chainRunDir chainRun/ chainRawDir chainRaw/ netDir net/ overDir over/

#Step 1, split NEW genome to 3kb chunks using UCSC faSplit tool python split-new-to-chunks.py

Step 2, write blat cmds

blat NEW vs OLD (old is the database, uses old 11.ooc file.), minScore=100 and minIdentity=95 python write-blat-cmds.py

this makes three files of blat cmds to be run on the cluster one is of same vs same chroms, these take a longer time to run, one is of chroms vs chroms one involves 'unplaced' chroms, may need to edit python script to get names right

[jmkidd@gl-login1 run-make-liftOver]$ wc blat*cmds 133948 1071584 38140926 blat.REST.cmds 40 320 10436 blat.SAME.cmds 349676 2797408 101646270 blat.UNK.cmds

check completion: [jmkidd@gl-login2 run-make-liftOver]$ dircnt_args blatRun/ blatRun/ contains 483664 files sum: 483664

Step 3

run liftUp to convert psl output files from blat chunks to original chromosome coordinates python run-liftUp.py

use python run-liftUp.py --file there are lots of cmds!

[jmkidd@gl3207 run-make-liftOver]$ wc liftUp.cmds 3268 19608 320211 liftUp.cmds

Step 4 run axtcCain to chain together alignments

python run-chain.py edit to be write-run-chain.py

then run runChain.cmds

Step 5 merge, sort, and split

runs chainMergeSort then chainSplit

python run-merge-sort.py

Step 6, run chainNet to make alignment nets out of the chains

python run-chainNet.py

Step 7 run netChainSubset

this gets only the chains that appear in the net

python run-netChainSubset.py

Step 8 cat together chains and gzip

python combine-over.py

Complete! liftover chain file is Dog10K_Boxer_Tasha_1.0.KP081776.1TocanFam3.1.chain.gz