| Author: | Gina Turco (gturco) |
|---|---|
| Email: | [email protected] |
| License: | MIT |
Contains a general pipeline for running ChipSeq analysis. This involves converting a sequence read archive file (sra) to a fastaq file. The Fastq file is then aligned to a reference genome and count data is obtained. Last but not least, comparisons between different groups of count data can be made with SICER for enrichment. For example differential expression between histone methlyation mark read counts of knockout and wild type can be compared.
Pipelines were developed in the Brady Lab at UC Davis
National Science Foundation, IOS-1238243 "Integrative Analysis of Plasticity in Cell Fate Determination in Plants"
Download the most recent code here:
git clone [email protected]:BradyLab/ChipSeq.git
Required Dependencies
- Dependencies were installed onto iplant AMI "ChipSeq" and are available through atmosphere with install instructions here
- Requires bwa, samtools, pysam, htseq, SICER, MACS, python2.7
-Create a new directory where the data will be stored