search

TheJacksonLaboratory / ATAC-seq

ATAC-seq Pipeline in conjunction with Duygu Ucar & Jacques Banchereau Laboratories
Creative Commons Attribution 4.0 International
11 stars 7 forks source link

ATAC-seq/auyar/ folder script unification #1

Open williamssanders opened 8 years ago

williamssanders commented 8 years ago

In ATAC-seq/auyar/, there are a number of bash shell scripts (*.sh) that need to be unified with the workflow described by auyar on Slide #5 in ATAC_intro.pptx.

  1. The order of the script operation needs to be established.
  2. A "workflow" bash shell script that runs all the subtasks of the workflow at once needs to be created.
  3. Valid testing data needs to be identified and used to validate the functionality of the new "workflow" script.
williamssanders commented 8 years ago

The workflow in ATAC-seq/auyar/ is as follows: fastQC.sh, trimmomatic.sh, and run_ATAC_pipeline.sh (which calls bwa_trimmomatic.sh, macs2_bwa_trimmomatic.sh, homer_bwa_trimmomatic.sh, and nReads.sh - in that order).

The file ATAC-seq/auyar_scripts.sh has been added to provide a "workflow" script with Torque/PBS support.

Pieces of it are currently untested due to immediate time constraints for data processing, but it should be close to functional, if buggy.