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
Maybe
flo, which helps runningUCSC liftover, might be helpful? https://github.com/wurmlab/flo