Question: ATACseqQC questions in R language
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gravatar for rsong
10 months ago by
rsong0
rsong0 wrote:

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.

atacseqqc • 162 views
ADD COMMENTlink modified 10 months ago by Ou, Jianhong1.1k • written 10 months ago by rsong0
Answer: ATACseqQC questions in R language
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gravatar for Ou, Jianhong
10 months ago by
Ou, Jianhong1.1k
United States
Ou, Jianhong1.1k wrote:

Hi,

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.

Jianhong.

 

 

ADD COMMENTlink written 10 months ago by Ou, Jianhong1.1k
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