Giter Club home page Giter Club logo

atac-seq-pipeline-test-data's Introduction

atac-seq-pipeline-test-data

Test data for ENCODE atac-seq-pipeline

Single ended dataset (ENCSR889WQX) and paired end dataset (ENCSR356KRQ) are subsampled down to 1/400 reads.

For genome data (/genome_data) sequences for chr19 and chrM are extracted from hg38 and mm10 and bowtie2 indices are built on them.

How to extract chr19 and chrM from original fasta

$ cd scripts
$ ./subsample_ref_fasta.sh

How to generate reference outputs

  1. Make sure that you have an executable cromwell-30.1.jar in your PATH.

  2. Specify correct file paths in subsample_fastq.sh and run to subsample test samples.

$ cd test_sample
$ ./subsample_fastq.sh
  1. Generate base reference outputs by running the following shell scripts. These test samples are subsampled down to 1/200 reads.
$ cd scripts
$ ./ENCSR356KRQ.sh
$ ./ENCSR889WQX.sh
  1. Wait until 2) is done. Link outputs of 2) to JSON files in test_sample/*.sh, run other shell scripts.
$ cd scripts
$ ./ENCSR356KRQ_disable_tn5_shift.sh
$ ./ENCSR356KRQ_no_dup_removal.sh
$ ./ENCSR356KRQ_no_multimapping.sh
$ ./ENCSR356KRQ_subsample.sh
$ ./ENCSR356KRQ_subsample_xcor.sh
$ ./ENCSR889WQX_disable_tn5_shift.sh
$ ./ENCSR889WQX_no_dup_removal.sh
$ ./ENCSR889WQX_no_multimapping.sh
$ ./ENCSR889WQX_subsample.sh
$ ./ENCSR889WQX_subsample_xcor.sh

atac-seq-pipeline-test-data's People

Contributors

leepc12 avatar

Watchers

 avatar  avatar

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    ๐Ÿ–– Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. ๐Ÿ“Š๐Ÿ“ˆ๐ŸŽ‰

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google โค๏ธ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.