Does anyone have any experience with PAF files (minimap2 output)? I don’t fully understand what my output means.
I’ve looked at the minimap2 explanation (https://github.com/lh3/miniasm/blob/master/PAF.md) but I want to use the data here to go back and extract regions in the genome that the gene target mapped to. I just don't know what specific columns to look at to accomplish this.
Here is a little snippet of a PAF file I have:
contig_25 522460 514241 515712 + GENE_TARGET 4988 1962 3649 258 1687 60
contig_26 413461 403718 406719 + GENE_TARGET 4988 17 3649 1762 3633 60
contig_44 24218 16005 17476 + GENE_TARGET 4988 1962 3649 258 1687 60
contig_52 244411 236199 237670 + GENE_TARGET 4988 1962 3649 258 1687 60
contig_57 1043583 1025163 1026895 + GENE_TARGET 4988 3046 4986 1376 2059 60
Is this saying that the gene target mapped to coordinates 514241 through 515712 on contig_25 but only coordinates 1962 through 3649 of the gene actually mapped to that contig? I guess I’m mostly confused on the descriptions for the coordinates and what they actually mean.
I think for my use case I have to use the gene target as the reference sequence as I am trying to extract homologous regions to sequences of interest. I.e., my project involves 90+ assemblies and I would like to extract the regions in the contigs where they map to the gene target. I used minimap2 to map the assemblies to the gene target, used sort and awk to get the best/high quality matches, converted PAF to BED format, and then used seqtk subseq to extract the sequences from the respective assemblies.
This is what I get when I use the gene target as a reference sequence:
GENE 4988 17 3649 + contig_26 413461 403718 406719 1762 3633 60
...
GENE 4988 3046 4986 + contig_57 1043583 1025163 1026895 1376 2059 60
Would I use columns 8 and 9 as the region range to go back and extract the sequences from?
