Ying Zhang comments

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                                            Ying Zhang

Is there a way to pull out the stability index matrix from the SC3 object?

Hi, Pati, I think you mis-understood my question. I have already run the full SC3 workflow, and I do have my object. So rather than simply plotting the stability index,...

Is there a way to pull out the stability index matrix from the SC3 object?

@pati-ni It will be great to include this function in future release. Thank you for taking my input. I also have a related question that might be off topic, however,...

Is there a way to pull out the stability index matrix from the SC3 object?

@wikiselev Thank you for the detailed reply. So for my SC3 workflow, I started with k estimation, then set up SC3 workflow with a series of K's surrounding the estimated...

KeyError during falcon_kit.stats_preassembly job

This makes sense, because the major difference between SGE and Torque is the time thing. I'll set the SGE option in the cfg file.

KeyError during falcon_kit.stats_preassembly job

OK, after I added the sge_option to the fc_run.cfg file, the entire process got stuck at the "preassembly report" step. I had to manually kill the falcon process, and push...

--use-nonoverlapping-peaks argument never used

I got the same error. So I checked the code, and it turns out the error is caused by an empty list. However, empty list in python doesn't mean "None",...

Failure: The Quiver algorithm requires a cmp.h5 file

This issue seems persist in the latest release of smrtlink and falcon. I downloaded falcon from https://github.com/PacificBiosciences/FALCON_unzip/wiki/Binaries, and I tried both SMRTLINK v 3.1.1 and v 4.0.0 This is the...