Viktor Petukhov

Hi, Can you please send your system details? Like OS version and hardware.

Hi @fengweimin-maker , Baysor gets NaNs in the covariance matrix, so it's not about it being symmetric. That's suspicious, I had put a lot of effort to check all possible...

That's totally understandable. If you can share the full log, and your config, I can check if there are some configuration errors. And if you can post just first several...

@fengweimin-maker , the log shows `scale std: 0.0`, and most likely that is the cause of the problem. It is probably caused by the gray image, indeed. Baysor does require...

The `scale` parameter is the expected radius of a cell (in pixels, in your case), and `scale-std` is how much cell sizes are allowed to deviate from it. I don't...

Hi! Thank you for the comment! > However, I am only getting a single tagged file called file_2.fastq.gz.tagged.1.fastq.gz instead of getting multiple demultiplexed files. Barcodes are encoded in read ids....

Hello, Thank you for the info! I will look at it in more details to give precise answer, but now it seems that you need to update the [white-list of...

Both these option use list of real barcode if the line is not commented. And in this case they produce very similar results. So, please try to comment the line,...

If two reads with different barcodes can belong to the same cell, dropEst will not deal with it properly and will split them into two cells. The easiest workaround would...

Hi! No, sorry. We still considering either to remove it or to completely rewrite.