Has anyone been able to figure out how to get breakdancer_max to run with the -o flag? Everywhere I've looked people have posted this same issue and I haven't seen any response to get it working and the devs don't respond to the issue, it's very frustrating.
-
-
I think I might have figured it out, if you add the prefix chr to the number it seems to run without a segmentation fault. This seems like poor coding and even worse documentation. -
I have not gotten the -o flag to work at all. At first, it could not read my bam file index (because I did not have one). Once I solved that I tried running it with -o 17 or -o chr17.
Neither produced a result. No errors, just made empty files. For the moment I am stumped.Comment
-
I got -o to work in breakdancer-max1.2, apparently they fixed it there. However there are many unknown (UN) svs called and for some reason running each chr individually then running in -t mode is magnitudes of order faster than running the entire bam without -o or -t which is rather shocking.Comment
-
Interesting. Good to hear the issue is resolved.
It appears I will not be able to get their latest version because of the methods they describe for installing it. Very frustrating. Maybe if I ask my computing admins very nicely they will do it for me...Comment
-
Right, if you have your own Ubuntu machine or a vm it's easy but if your admins are anything like mine good luck because their github package is messed up and so source compiling doesn't work without a lot of work.Comment
-
NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...10-30-2026, 06:46 AM -
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM
Comment