We are doing ATACseq in kidney field and found ATACseqQC package and was very excited to use it for our data QC. I am new to this R and bioinformatics so my questions are what kind of files do you use for this package, if I use mouse tissue, what library I need to install besides ATACseqQC? Thank you very much for the help.
Thank you for trying ATACseqQC package. In the vignette of ATACseqQC, we list the packages for human. The following is the code for preparing the packages of mouse:
library(BiocInstaller) biocLite(c("ATACseqQC", "ChIPpeakAnno", "MotifDb", "GenomicAlignments", "BSgenome.Mmusculus.UCSC.mm10", "TxDb.Mmusculus.UCSC.mm10.knownGene"))
You can skip the conservation parameters in splitGAlignmentsByCut function. If you want to have a try with the conservation scores, please refer mm10 phastCons data for use with ATACseqQC
Have a good luck.