jianhong / ATACseqQC

ATAC-seq Quality Control

Home Page:https://jianhong.github.io/ATACseqQC/articles/ATACseqQC.html

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Adjust the read start sites of mouse data

vibook opened this issue · comments

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.

library(BSgenome.Mmusculus.UCSC.mm9)
which <- as(seqinfo(Mmusculus)[seqlev], "GRanges")