PairedTag Data Analysis for Adult Mouse Brain

Data preprocess and alignment from Johnny

• https://github.com/zwang0715/Paired-Tag

Download codes

1. git clone https://github.com/beyondpie/amb_pairedtag [local_directory]
2. cd [local_directory] and git submodule update --init --recursive
   • We have one submodule named extratools in the repo, so use this command to pull those codes.

genome annotations

1. We use mm10 / GRCm38 for alignment.
2. We mainly use GRCm38.p6-M25 gene annotations from https://www.gencodegenes.org/mouse/release_M25.html.
3. Promoters are usually followed the definition of up/down stream 1kb of TSSs.

Code organization

tmpRpkg

One temporary R package named tmpRpkg right under the project to enable global sharing of common variables and functions.

• I follow the R package book to manage the package.
  • run devtools::document() to update the export NAMESPACE
  • run devtools::load_all() to fast update the package for use. If failed, try run unload("tmpRpkg") firstly.
  • run devtools::install() can install the package immediately.
• detach("package:tmpRpkg", unload=TRUE) and then library(tmpRpkg) to reload the updated/re-installed package.

tmpPypkg

One temporary Python package named tmpPypkg.

1. Update PYTHONPATH

   export PYTHONPATH="/your_local_dir/amb_pairedtag:${PYTHONPATH}"
       

2. Then import tmpPypkg in Python.

Scala

1. Set up env.
   • Use conda/mamba to install java. Here we use Java version 22.0.1 (>= 22 should be OK.) mamba install conda-forge::openjdk=22.0.1
   • Then use couriser to manage scala’s tools, like sbt (project manager), scala and so on. Check the installation details here: https://get-coursier.io/docs/cli-installation
2. Compile the project
   • Under the project root, we can use sbt interactive way to compile the project. sbt then compile
   • Under the project root, we can also run sbt compile in terminal.
   • [Optional] Assemble: use sbt assembly to assemble the scala codes into target directory.
   • For now, I put bioscala and project-related scala files under src/main/scala. And for each subtask, like CallPeak, DataPreprocess and so on, I put them into the correponding subdirectories. projects can show all the project we have, and project [some subproject] can change the default project to the one we want.
3. Run
   • Under the interactive sbt, use run to run multiple main functions, it will output the multiple main functions you can run, and then you can insert the number to run the specific one.
   • console can provide the scala REPL
   • If you assemble the projects, you can then java -cp target/scala-verion/version.jar someMain someArgs to run some particular functions.