Jian Zhou
Jian Zhou
It will be padded with 500 Ns on either side. How the Ns will affect the model prediction is largely tested and thus not recommended (in the training the Ns...
Hello- My script loads the chromatin feature predictions and do this ``` rank = np.arange(100) Xreducedall = [np.tensordot(Xfor[:,:100,:],np.exp(i*rank),axes=([1],[0])) for i in [-0.01, -0.02, -0.05, -0.1, -0.2] ] + \ [np.tensordot(Xrev[:,:100,:],np.exp(i*rank),axes=([1],[0]))...
Hi, Hope this helps: 1. You can use all mutations but for computational efficiency, but I recommend focusing on variants within 10kb or 20kb to TSS. Mutations that are further...
I think you are asking about the variation potential directionality score which is the sum of predicted mutation effects of all potential mutations - right? The sum is used to...
I see that is an interesting question. That will be equivalent to the square of the variation potential directionality score - it can probably have an interpretation as the size...
Did you try `git pull` the newest code? I just made a commit to fix a bug that may cause this.
You can get the files from ENCODE project here http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgDnaseUniform/ http://hgdownload.soe.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/ On Thu, Feb 20, 2020 at 5:27 AM Licko0909 wrote: > 874 file from here: > > https://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/narrowPeak/ >...
The full list of URL is also available here (https://static-content.springer.com/esm/art%3A10.1038%2Fs41588-019-0420-0/MediaObjects/41588_2019_420_MOESM9_ESM.xlsx). Even though some of the URLs are no longer valid as of now even though you should be able to...
The website only contained variants with >0.3 predicted log fold change in at least one tissue while the code provides all predictions regardless of their effect size. For your second...
Yes you should have no problem applying Beluga it to hg38 sequences. but we do have a newer and much improved model Sei that you might want to use instead...