Yang Shi
Yang Shi
Hi, thanks for developing such a awesome tool! I download ”gene level copy number“ using TCGAbiolinks, and I supposed there are five values: -2(del),-1(loss),0(diploid),1(gain),2(amp). But when I download the data.type...
Hi, I want to get the allele frequency of indels from Strelka using samtools mpileup, but I found there are some difference in ref_count and alt_count between these two methods....
Hi, I have multiple 30X WGS data and want to try AA on it. As mentioned in other issues, 30X is too large for AA and downsampling is recommended. But...
Hi Diamond developers, Thanks for developing such an awesome tool. I'm using Diamond to analyze mass spec data and all of them are very short peptides (usually 8-12 aas). I...
Hi, I'm using guess_baits.py to decode the target region of my bam file. When I run it, it throws out an error: `Traceback (most recent call last): File "/home/shiyang/softwares/anaconda3/envs/cnvkit/lib/python3.8/concurrent/futures/process.py", line...
Hi, First thanks a lot for developing such an awesome package! It gives me a lot of help! I noticed that only pearson correlation is allowed now, is it possible...
HI, First thanks for developing such an awesome tool. I want to apply it on my WGS data to call somatic CNA. However, when I tried this step: conda env...
Hi FACETS developers, When I use FACETS on my WES data, I realized that the ploidy estimate (fit$ploidy) can be much different from the CN segment profile. Below I attached...
Hi, I am using FACETS to estimate the ASCNV for my WES data. I can get the absolute copy number for each segment now, but I want to call recurrent...
Hi I want to use the copy number information estimated by FACETS to analyze clonal evolution with PhyloWGS. In addition to some basic metrics of each segment, PhyloWGS requires another...