Example data does not work as stated because it is still under development

[ricardoharripaul]

Hi, I am trying to run the example data but I received an error stating the function is still underdevelopment.

conclusion <-

• atacPipe2(

• # MODIFY: Change these paths to your own case files!
  

• # e.g. fastqInput1 = "your/own/data/path.fastq"
  

• case=list(fastqInput1 = system.file(package="esATAC", "extdata", "chr20_1.1.fq.gz"),
  

•           fastqInput2 = system.file(package="esATAC", "extdata", "chr20_2.1.fq.gz")), 
  

• # MODIFY: Change these paths to your own control files!
  

• # e.g. fastqInput1 = "your/own/data/path.fastq"
  

• control=list(fastqInput1 = system.file(package="esATAC", "extdata", "chr20_1.2.fq.bz2"),
  

•              fastqInput2 = system.file(package="esATAC", "extdata", "chr20_2.2.fq.bz2")),
  

• # MODIFY: Change this path to an permanent path to be used in future!
  

• #       refdir = "./esATAC_pipeline/refdir",
  

• #       tmpdir = "./esATAC_pipeline/intermediate_results", 
  

• # MODIFY: Set the genome for your data
  

• genome = "hg19")
  

Error in atacPipe2(case = list(fastqInput1 = system.file(package = "esATAC", : this function is still under developing

[rrashford]

I also received this error upon trying to run with my own data.

[linzhangTuesday]

Hi any update on this? atacPipe2 also gives an error of "this function is still under developing".

[hyjforesight]

here are the solutions from the authors.

We are developing a new version of esATAC. Some functions are not robust so we still do not provide them.

Currently, there are two solutions.

(1) Use "atacPipe" for each sample instead.

You can also get the same quality control, peak file and fragment file by applying atacPipe to case sample and control sample respectively.

Then, you can compare the peaks or fragments between case and control samples with some tools like bedtools by yourself .

(2) Use "atacPipe2" in older versions in esATAC

Install R-3.6.1 first and install bioconductor 3.10

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.10") install esATAC

You can follow the instructions and manual in older version:

http://bioconductor.org/packages/3.10/bioc/html/esATAC.html