How to merge chain file from different chromosome

[zhoudreames]

I split the genome into 20 chromosomes and then ran nf-Lo with blat alignments for each chromosome. I don't know how to merge all chain files into one chain, can you help me ?

[RenzoTale88]

@zhoudreames thank you for using nf-LO!
My suggestion is to run nf-LO on the whole genome at once and leave nf-LO to combine the data itself. nf-LO split the genome in fragments of different sizes and then combine.

Having said that, if you want to proceed with the individual chains you can combine the files using chainMergeSort and chainSplit in sequence:

chainMergeSort *.chains | chainSplit run stdin -lump=1 
mv run/000.chain ./merged.chain

Then generate the net file:

chainPreNet merged.chain source.sizes target.sizes stdout |
        chainNet -verbose=0 stdin source.sizes target.sizes netfile.net /dev/null 

And finally create the resulting liftover:

netChainSubset -verbose=0 netfile.net merged.chain stdout | chainStitchId stdin stdout > liftover.chain

Hope this helps

Andrea

[zhoudreames]

Thank you for your Detailed description， I try it.