Question: liftOver function in rtracklayer package is not working
gravatar for beausoleilmo
14 months ago by
beausoleilmo0 wrote:

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: 

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:
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? 

ADD COMMENTlink modified 14 months ago by Michael Lawrence10k • written 14 months ago by beausoleilmo0
gravatar for Michael Lawrence
14 months ago by
United States
Michael Lawrence10k wrote:

The ranges to lift over are coming from the GFF file, so that should be the GRanges, and that's what import() gives you. The sequence names in the GFF file have to match the names in the chain file. My guess is that you either need to rename the sequences in the GRanges or maybe you don't even have the right chain file.

ADD COMMENTlink written 14 months ago by Michael Lawrence10k

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? 

ADD REPLYlink written 14 months ago by beausoleilmo0
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