Hi,
Thank you for sharing this wonderful method. I was able to run the first step smoothly but I am having difficulty second step onward. I tried running the tumor_purity_estimation first, and I keep getting the same error with adata ending up with zero spots in the end. I have attached a screenshot of the error. I looked into it further, and it seems like the filtration happens at the snp_umi filtration step shown in second screenshot.
The function has it set as 50 and my cellsnp_a and b files only have around 1 snp summed across locus per spot. I was not sure if this is to be expected so I also checked the DP and AD mtx files and these don't seem that bad with following metrics:
spots: 22298
SNPs : 22114
median total depth per spot: 1701.5
fraction spots with depth >= 5: 0.9999103058570276
fraction spots with depth >= 10: 0.999416988070679
I wanted to ask what would be some ways to assess if the step 1 was run okay and the generated cellsnp_a and b files have numbers in the right range. I am planning on relaxing that parameter and running it on all spots just to see but wanted to know your thoughts on it. Thank you!!
Hi,
Thank you for sharing this wonderful method. I was able to run the first step smoothly but I am having difficulty second step onward. I tried running the tumor_purity_estimation first, and I keep getting the same error with adata ending up with zero spots in the end. I have attached a screenshot of the error. I looked into it further, and it seems like the filtration happens at the snp_umi filtration step shown in second screenshot.
The function has it set as 50 and my cellsnp_a and b files only have around 1 snp summed across locus per spot. I was not sure if this is to be expected so I also checked the DP and AD mtx files and these don't seem that bad with following metrics:
spots: 22298
SNPs : 22114
median total depth per spot: 1701.5
fraction spots with depth >= 5: 0.9999103058570276
fraction spots with depth >= 10: 0.999416988070679
I wanted to ask what would be some ways to assess if the step 1 was run okay and the generated cellsnp_a and b files have numbers in the right range. I am planning on relaxing that parameter and running it on all spots just to see but wanted to know your thoughts on it. Thank you!!