NetFilterNonNested.perl input

[aaannaw]

Hello
I have generated target.net query.net file using chainNet but now when I am trying to run NetFilterNonNested.perl to filter but I am confused about the input files ref.query.net.gz. Could you give me any suggestions?
NetFilterNonNested.perl -doUCSCSynFilter -keepSynNetsWithScore 5000 -keepInvNetsWithScore 5000 ref.query.net.gz > ref.query.filtered.net

[MichaelHiller]

The input must be a classified net file (with information about inversions/translocations etc), as produced by netClass.

For filtering, we now often use a minTopScore threshold of 100000 (doUCSCSynFilter is much stricter) and keep syn/inv nets that score above 5000.
Hope that helps

[aaannaw]

Hello
Could you give any command about netClass? I run chainNet with the command chainNet -rescore all_output_sort.chain target_genome.sizes query_genome.sizes target_genome.prenet query_genome.prenet and generated target.net query.net file. What is the netClass input ?

[MichaelHiller]

After chainNet, we run
netSyntenic in.net out.net
and the resulting net is the input for netClass
netClass [options] in.net tDb qDb out.net
tDb - database to fetch target repeat masker table information
qDb - database to fetch query repeat masker table information

Michael