Question: How to transfer gff3 annotation from scaffolds to reference genome?
gravatar for Bea
21 months ago by
Bea0 wrote:

Good afternoon everyone,

I am doing genome skimming to retrieve microsatellite loci from my genomic dataset.

To start, I filtered the raw Illumina reads (2x150bp) with Trimmomatic and then did an assembly de novo with SPAdes. Then, I mapped the SPAdes scaffolds to the reference nuclear genome for my study species. Using the scaffolds that mapped to the reference, I ran msatcommander with which I identified microsatellite loci.

From the msatcommander output, I know the start/end position within scaffolds of my microsatellite loci, so I created a gff3 file. I can visualize the microsat annotation in IGV when opening the the scaffolds file as genome and the gff3 file as track. The gff3 file is ok.

I now want to translate the microsatellite loci coordinates relative to my scaffolds to coordinates relative to the whole genome I am using as a reference. Remember that I mapped my scaffolds to the reference already, so I think it is quite an easy step, but by looking around I could not figure out a quick way out of it.

I checked this answer and I think it is really close to what I need, but not exactly.

If you have any input on this, that would be great! Thank you, Bea

ADD COMMENTlink written 21 months ago by Bea0

Maybe flo, which helps running UCSC liftover, might be helpful?

ADD REPLYlink written 21 months ago by jean.elbers1.5k
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