Closed TheSallyGardens closed 4 years ago
Hi,
SnapATAC does remove duplicates when running snaptools pre
but you do not need to remove duplicates before snaptools pre
.
Hi,
SnapATAC does remove duplicates when running
snaptools pre
but you do not need to remove duplicates beforesnaptools pre
. Thank you for your answer! What software do you use to remove duplicates? Does snapATAC have statistically duplicated information?
Yes,
SnapTools removes duplicates for each cell separately. In a given cell, two fragments are considered to be duplicate if their gnomic position and strand information is identical. The duplicate information will be stored in the meta data inside the resulting snap file. You can access the quality of each barcode in SnapATAC:
library(SnapATAC)
x.sp = createSnap("your_snap_file.snap", sample="your_snap_file")
x.sp@metaData
## barcode TN UM PP UQ CM
## 1 AAAAAAAAAAAAAAAA 102 44 44 44 0
## 2 AAAAAAAAAAAAAAAC 10 6 6 6 0
## 3 AAAAAAAAAAAAAAAG 3 0 0 0 0
## 4 AAAAAAAAAAAAAAAT 2 1 1 1 0
## 5 AAAAAAAAAAAAAACA 6 1 1 1 0
## 6 AAAAAAAAAAAAAACC 1 1 1 1 0
The duplicate ratio can be calculated as:
1 - (x.sp@metaData[,"UQ"] +1) / ( x.sp@metaData[,"PP"] + 1)
Yes,
SnapTools removes duplicates for each cell separately. In a given cell, two fragments are considered to be duplicate if their gnomic position and strand information is identical. The duplicate information will be stored in the meta data inside the resulting snap file. You can access the quality of each barcode in SnapATAC:
library(SnapATAC) x.sp = createSnap("your_snap_file.snap", sample="your_snap_file") x.sp@metaData
## barcode TN UM PP UQ CM ## 1 AAAAAAAAAAAAAAAA 102 44 44 44 0 ## 2 AAAAAAAAAAAAAAAC 10 6 6 6 0 ## 3 AAAAAAAAAAAAAAAG 3 0 0 0 0 ## 4 AAAAAAAAAAAAAAAT 2 1 1 1 0 ## 5 AAAAAAAAAAAAAACA 6 1 1 1 0 ## 6 AAAAAAAAAAAAAACC 1 1 1 1 0
The duplicate ratio can be calculated as:
1 - (x.sp@metaData[,"UQ"] +1) / ( x.sp@metaData[,"PP"] + 1)
Thanks!
Hi. I have finished cellrange-atac pipeline,Is it necessary to remove duplication for BAMfile?
I know that snapATAC do not remove duplication.