How to plot the gap distribution of contigs wrt to reference genome
I have a contigs file that I generated using Minia and then I have used Minimap2 to map these contigs again to the reference genome. Now I want to plot the gap distribution i.e. gap distance of the set of contigs with respect to the positions in the reference genome.
For example: something like , if there are m contigs obtained from the Minia, then X axis will show 0 to m-1 gap points (in an ideal case where there is no overlap between the contigs and the contigs are aligned back to back without space).
The file from minimap2 looks like this:
0 17679 0 17679 + NZ_BCML01000091.1 39426 18736 36415 17679 17679 60 NM:i:0 ms:i:35358 AS:i:35358 nn:i:0 tp:A:P cm:i:3274 s1:i:17675 s2:i:49 de:f:0 rl:i:75 cg:Z:17679M
where the 1st column is the contig ID and 8th and 9th column show the start and end position of the contig on the reference genome.
I have used the samtools for obtaining a length distribution plot, but not understanding how to do a gap distribution plot. Thank you for all the help.
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