Building reference gene panel, advise about uncalled HOT 4 OPEN

Opps, I just discovered your suggestions for masking: https://github.com/skovaka/UNCALLED/tree/master/masking
I will try that.

from uncalled.

Sorry you're having trouble! Reference masking is a good idea. Just to make sure, does your reference extend all the way to the ends of your targets? I'd also recommend running UNCALLED on those "regular cas9" reads to see if they can map to you reference in standalone mapping mode (see "Fast5 Mapping" in the readme). I haven't worked with the mouse genome before, but if you're still having trouble after masking you could send me your reference and I could take a look.

from uncalled.

I am not sure if masking helped. The regular cas9 reads definitely map to the reference. But we don't see an improvement in yield compared to whole genome sequencing. What is the best way to send you the reference so you can check it out?
Thank you!

from uncalled.

You can email your reference to skovaka1 jhu.edu. Other factors which could reduce your enrichment could be read lengths or your computer's CPU, so if you could let me know the lengths of your on-target reads and your CPU model that could be helpful. On Ubuntu running the command grep "model name" /proc/cpuinfo should return the model name.

from uncalled.