EvanTarbell
EvanTarbell
> > You can use HMMRATAC instead now, which is a substitution of MACS2 spcific designed to ATACseq. It is developed by Tao Liu too. > > Thanks, Sounds good!...
Thanks @pratarora !! Great catch!
State 0 is the background State, State 1 is the nucleosome state and state 2 is the open state (assuming default -k value) Pi is the starting probability, ie the...
Hi, A few things. 1. the fragment length distribution is off. You don't see any multi-modal behavior in your plot. Generally, this indicates that there is something wrong with the...
This is a bug. I recently added a function to filter the peaks based on --threshold, but the --score all option creates a string with all scoring systems that are...
Can you generate a fragment length distribution plot for these datasets? Part of me suspects that there might be datasets with an incomplete fragment distribution, which is causing a negative...
Which of the samples are failing and which ones succeed? and can you attach the log files that are generated?
So I still think that --trim would solve this problem but it turns out that i dont apply the procedure until after the EM step (ie after the error you...
This seems like a threshold problem. It might be that for this dataset, the default thresholds for reporting peaks might be too stringent (for both HMMRATAC and MACS). Try lowering...
Thanks for the report! I'll look into fixing that ASAP.