Viraj Deshpande

Hello asalcedo31, Thank you for raising the issue. It will help me improve the software and documentation. I suspect this is a performance issue. The warning is not the source...

Hello Adriana, You should be able to access the web interface now, but I working on a more permanent configuration of the server. It is fantastic you were able to...

If you see the edge going from the end of the amplicon to the beginning and the intermediate segment appears roughly intact (or at most some deletions) that should be...

Generally speaking, if it is a high copy focal amplification, even if AA fails to reconstruct a complete cycle, it is highly likely to be of ecDNA origin. By ecDNA...

Hi Alvin, Thanks for trying AA. Your interpretation is correct. In the clustered mode, AA treats all seed intervals in the input bed file as part of the same amplicon....

Hello Shangxin, Can you try this branch and let me know if this shows an improvement in runtime? Best, Viraj

@alvinwt, thanks for pointing this out. I forgot to include the link in my previous message. Here: https://github.com/virajbdeshpande/AmpliconArchitect/tree/runtime_discordant_clustering

Hello @riazgillani , Apologies for the slow reply, I am not sure why it is reporting this error. I will look into this and reply back in about a week.

Hi @songxiaoning, can you try downsampling the file to say 5X or 10X coverage. This will give you a BAM file around 10-15GB. The best way to downsample is by...

Does this link work: https://drive.google.com/drive/folders/0ByYcg0axX7udeGFNVWtaUmxrOFk?resourcekey=0-WW7hTVXmgiBIsiwMP14ERA&usp=sharing