Jens Luebeck

Hi Rong, Mosek is used internally by AA to solve a convex optimization problem to resolve the set of decomposed structures from the NGS-derived breakpoint graph. Unfortunately, it is not...

Glad to hear it worked out, Rong. I believe the breaking changes to Mosek were introduced starting in version 9.

Hi Rong, Sorry to hear about the issues with Mosek. I would speculate that this is indeed some sort of issue caused by using the slightly newer version of Mosek....

Hi Rong, Thanks for letting me know. If there are new error messages, different from the original, please feel free to open an Issue and I'll take a look. Best...

Hi, Thanks for reporting this. After restructuring the data repo, we realized that this error arose. We will be updating the docker image soon to correct the bug in the...

Hi, The regions identified by CNVkit are filtered by the AA script 'amplified_intervals.py', to remove regions that are too small to be candidate AA amplicons, too low in CN, or...

Hi Heng, The warning about font is harmless and does not affect results. Regarding the chr1 amplicon. AA uses copy number seed regions which are identified to have significant amplifications...

Hi, Downsampling is performed by AA on the fly, and thus you do not need to worry about running any custom downsampling/creating a new BAM file on your own. Setting...

Hi Yang, That sounds very reasonable regarding the downsampling strategy you proposed. Are you using PrepareAA + CNVKit to generate the CNV seeds (highly recommended)? If so, to optimize your...

Hi Yang, That is strange that you got so many CNV seeds. What is the range of CNs estimated for these seeds? If you would like please feel free to...