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
-
CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM
Comment