Entering edit mode
Hello Rory,
I am using diffbind to extract the raw counts for my PEAKS. I used the function
myData.RawCount <- dba.count(myData, score=DBA_SCORE_READS)
myData.RawCount.value <- dba.peakset(myData.RawCount, bRetrieve=TRUE, writeFile="../RawReads.txt")
I am using it for Single-cell ATAC seq analysis. But when I open the file, I see that the file have no Zeros. Its only 1 and value above 1. But for peaks that does not have any count, shouldn't it be 0? Why there are 1 instead of 0s.
When I use, the bedtools multicov for counts, it gives me lots of zeros (as I would expect in single-cell)
Thank you.
Best Regards,
Syed
Asking the following question just for a bit of more clarification,
I have two sets of single cells, each composed of 96 cells. When using bedtools multimap, I combine the peakset from all these 192 cells and then count the overlapping peaks to have the count for each cell. I was wondering, is this the same approach that Diffbind takes. Because I found some dissimilarity in the count of Diffbind and bedtools multicov.
Thank you again.
Best Regards,
Syed