Rongxin Fang

Hello, You can select cells based on "coverage" and "promoter ratio" - percentage of reads mapped to promoters per cell ``` > library(GenomicRanges); > system("wget http://renlab.sdsc.edu/r3fang/share/Fang_2019/MOs_snATAC/genes/promoter.bed"); > promoter.df = read.table("promoter.bed");...

"promoter.bed" is a list of promoters in mouse genome (mm10), you might need to find another list for mm9

Hi, I have create a folder that contains reference files required for the analysis: http://renlab.sdsc.edu/r3fang/share/github/reference/ Inside the mm9 folder, you will find the [gencode.vM1.annotation.gtf](http://renlab.sdsc.edu/r3fang/share/github/reference/mm9/gencode.vM1.annotation.gtf) file which is GENCODE annotation for...

sorry, it is a typo. should be `gene.gr

Hi there, Thank you for your question. Currently, it does not support that functionality. What would be the application for that if it is possible to extract any subset of...

Hi, Thanks for the clarification, I don’t know if i full understand our question. SnapATAC is able to subset or combined multiple samples easily. For example, this is one example...

Hi Emma, Have you add the `pmat` to the snap file? In order to let SnapATAC load the cell-by-peak matrix, you will need to first add the `pmat` to the...

Can you install the most updated version and try it again? this was an error in the old version -- Rongxin Fang Ph.D. Student, Ren Lab Ludwig Institute for Cancer...

hi, I am sorry for the error. this might be because you have stored the whole space as “RData” and when you load the image, the previous environment variable will...

Hi Molly, This is caused by a version issue between python 2 and python 3. I will try to fix it this or next week. I think it will affect...