Open yeswzc opened 4 years ago
Hello,
How many cells do you have for cluster_i?
The number of cells varied across clusters, most of them have hundreds of cells.
> sort(table(x.sp@cluster))
10 11 2 12 13 6 1 4 3 9 7 8 5
15 139 214 227 405 407 447 788 835 846 891 1080 1470
Thank you!
I do see the same thing for some clusters with my dataset. I tuned the parameters and found that lowering the bcv made some regions appeared as significant ones. I am wondering whether this tuning is valid, or is the dispersion itself is actually lower for ATAC-seq compared with RNA-seq. Thanks.
@qingnanl , thank you! I am also not sure if it is ok to tune bcv. I followed the vignette of 10X Adult Mouse Brain, in which the author indicated bvc = 0.4 for human, 0.1 for mouse. Hope @r3fang could help.
Hi, Do anyone know why I identified no DARs under the threshold of FDR<0.05 using snapATAC ?
I analyzed my human 10x genomics scATAC-seq data according to '10X Adult Mouse Brain' tutorial and tried to find DARs by:
However, no significant DARs were identified for each cluster. Do anyone have the same problem?
Thanks!