I'm trying to use rtracklayer to run a liftOver. I have the GFF file as well as the fasta file for my reference genome. I'm not able to make lifOver work. It runs, but no sequence match:
library(rtracklayer)
ch = import.chain("~/Desktop/LiftOver test/geoFor1ToTaeGut1.over.chain")
Warning message:
In if (is.null(value)) { :
closing unused connection 3 (~/Desktop/LiftOver test/geoFor1ToTaeGut1.over.chain)
gff.mgf = import.gff3(con = "~/Desktop/LiftOver test/ref_GeoFor_1.0_top_level.gff3")
liftOver(x = gff.mgf,
chain = ch)
Discarding unchained sequences: NW_005054297.1, NW_005054298.1, NW_005054299.1, NW_005054300.1, NW_005054301.1, NW_005054302.1, NW_005054303.1, NW_005054304.1, NW_005054305.1, NW_005054306.1, NW_005054307.1, NW_005054308.1, NW_005054309.1, NW_005054310.1, NW_005054311.1, NW_005054312.1, NW_005054313.1, NW_005054314.1, NW_005054315.1, NW_005054316.1, NW_005054317.1, NW_005054318.1, NW_005054319.1, NW_005054320.1, NW_005054321.1, NW_005054322.1, NW_005054323.1, NW_005054324.1, NW_005054325.1, NW_005054326.1, NW_005054327.1, NW_005054328.1, NW_005054329.1, NW_005054330.1, NW_005054331.1, NW_005054332.1, NW_005054333.1, NW_005054334.1, NW_005054335.1, NW_005054336.1, NW_005054337.1, NW_005054338.1, NW_005054339.1, NW_005054340.1, NW_005054341.1, NW_005054342.1, NW_005054343.1, NW_005054344.1, NW_005054345.1, NW_005054346.1, NW_005054347.1, NW_005054348.1, NW_005054349.1, NW_005054350.1, NW_005054351.1, NW_005054352.1, NW_005054353.1, NW_005054354.1, NW_005054355.1, NW_005054356.1, NW_00505... <truncated>GRangesList object of length 457437:
[[1]]
GRanges object with 0 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[[2]] ...
Is there a way to run liftOver using a GFF file or a reference genome?
In the help documentation:
x => The intervals to lift-over, usually a GRanges.
How do you create this GRanges object and from which file? A fasta? A GFF?
I think your right and it's only the names inside the chain and the .GFF that are not matching. I guess in the end, you just have a file with the matching information from the .chain file. For example, I want to get the matching chromosomes from the Zebra finch genome to Darwin's finch genome: geoFor1ToTaeGut1.over.chain
Is that correct?