Adjust the read start sites of mouse data
vibook opened this issue · comments
Rose Park commented
Hi,
I installed ATACseqQC to offset ATAC-seq aligning.
The example code in the Guide is for human data.
I downloaded BSgenome.Mmusculus.UCSC.mm9 but I'm struggling with another part.
seqlev <- "chr1" ## subsample data for quick run
which <- as(seqinfo(Hsapiens)[seqlev], "GRanges")
I want to offset all sample data and I cannot figure out how to change seqinfo() instead of Hsapiens.
Thank you.
JIANHONG OU commented
library(BSgenome.Mmusculus.UCSC.mm9)
which <- as(seqinfo(Mmusculus)[seqlev], "GRanges")