Comments (2)
@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
from nf-lo.
Thank you for your Detailed description, I try it.
from nf-lo.
Related Issues (20)
- Process requirement exceed available CPUs -- req: 2; avail: 1 HOT 9
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