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mahulchak / mlift

A mummer based genomic coordinate liftover tool
GNU General Public License v3.0
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Empty query coordinates in lifted.txt? (request example .bed file) #1

Open lokeyCEU opened 3 years ago

lokeyCEU commented 3 years ago

I'm seeming to run into trouble with the bed file. Could we get an example for what is expected in the bed file? Is it simply the chromosome name the start BP (1) and then the length of said chromosome?

For example my bed starts like this 1 1 178720847 2 1 109423767 3 1 121101644 4 1 101460260

Am I interpreting this correctly?

lokeyCEU commented 3 years ago

For more context I ran the following commands to do a lift-over from one assembly to another for the same species.

` nucmer --prefix ref2q CS_Ragoo35.fa CSV4gen.fa

delta-filter -r -q ref2q.delta > ref2q.rq.delta

/programs/mlift-0.1/mlift ref2q.delta CS_Ragoo35.chr.bed l

cd mm

nucmer --prefix ref2q.mm ../CS_Ragoo35.fa ../CSV4gen.fa

/programs/mlift-0.1/mlift ref2q.mm.delta ../CS_Ragoo35.chr.bed l `

There were no errors during either run but the lifted.txt looks like this for both runs

REF_CHROM   REF_START   REF_END Q_CHROM Q_START Q_END
1   1   178720847   CSV4s0001_60700 NA  0
1   1   178720847   CSV4s0001_60700 0   NA
1   1   178720847   CSV4s0002_307280    NA  0
1   1   178720847   CSV4s0002_307280    0   NA