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# Astrocyte ChIPSeq Example

This workflow carries out a simple ChIPSeq alignment and peak calling using 
*BWA* and *MACS 1.4*. One or more FASTQ files containing reads from a ChIPSeq
experiment can be selected as input. For each file this workflow:

  1. Aligns the reads to a selected genomic reference using BWA aln.

  2. Converts BWA's native output into SAM format.

  3. Sorts and indexes the SAM file, and converts into binary BAM format using 
  Picard.

  4. Performs ChIPSeq peak calling using MACS 1.4, with simple `--no-model` and 
  `--single-profile` options. Wig files are produced as well as standard
  spreadsheet output.


## Workflow Parameters

  * **fastq** - Choose one or more ChIPSeq read files to process. All should be
  ChIP files - i.e. there is no control. Each file will be processed as an
  independent sample.

  * **index** - Choose a genomic index to use as a reference for alignment of
  ChIPSeq reads. A variety of options are available for human and murine
  samples.

## Visualization App

The example visualization app demonstrates integration of Shiny into astrocyte
by implementing a simple file chooser that access the output of the workflow.

## Test Data

The test data directory of this workflow package includes a subset of reads from
Chr19 for a CTCF ChIP in a G1E cell line.

Originally made available as example data for the Galaxy ChIP-Seq exercises
at [https://usegalaxy.org/u/james/p/exercise-chip-seq]


## Credits

This example worklow is derived from original scripts kindly contributed by the
Xu lab, Children's Research Instiute at UT Southwestern.