SAMtoBAM

Although it is a repetitive region, it doesn't technically contain tandem repeats. The region is a isolated transposon which contains inverted repeats on either end but they are only 300bp...

Hi Moritz, Thanks for the help here So I tried what you suggested, added a bed file (below) to the calling process encompassing the entire region containing the transposon. Some...

Awesome, I'll keep an eye out for this post-processing script For now, at least in these simple homozygous cases, all the overlapping chunks appear to contain simple, single, large events...

Me again, Just to note, I just tried it with NGMLR, as the overlap aggregation of the minimap2 calls didn't work as well as I hoped, and sadly using NGMLR...

Below is a histogram of the proportion of methylated reads at each position along the genome  I have this sort of pattern, where the 0.5 occurs just...

Yes it is a fasta file for the query assembly I have already done it with minimap2 using the asm5 option I was wondering if MashMap would perform differently, particularly...

Genome wide alignments is exactly what I want, its just I can have 3-4 phased haplotypes assembled within a single polyploid genome. Plus with the default 'map' filter I should...

Hi there, Sorry for the late reply. I think 'make hardier' is the appropriate title, it has been something in the back of my head for a bit now So...

Added v3.8 now which should be much more hardier Thanks again

Hi there, Do you have the alignment files? Can you have a look at the .coords file and see what is in there? Or send me them and I will...