dipseq

Code for handling data from domain insertion library sequencing.

Data Formats

• Read data is expected in FASTQ format.
• Alignments are output in SAM and converted to BAM for analysis.
• Final output of variant calling is a CSV file.

Python Dependencies

• Basic dependencies
• scipy numpy pandas biopython
• Dependencies for enrichment analysis
• rpy2

External Dependencies

• Java runtime (for BBmap).
• C compiler (GCC, for fastq-grep installation).
• BBMap toolkit for fast filtering and alignment of reads.
• http://sourceforge.net/projects/bbmap/
• fastq-tools for regex trimming of reads.
• You may need to install from source for most recent version.
• https://github.com/dcjones/fastq-tools
• R, DESeq
• http://bioconductor.org/packages/release/bioc/html/DESeq.html

Installation

0. Make sure that you have GCC and the Java runtime installed.

• If you are on a Macintosh, the easiest way to do this is to install the developer tools.
• You can do this by running xcode-select --install from the command line.
• You can also install the Java runtime independently by following these instructions.
• https://www.java.com/en/download/help/mac_install.xml

1. Install the BBMap toolkit.

• Download the project zip from sourceforge (link above).
• Unzip and move the unzipped folder somewhere permanent (e.g. make a ~/bin directory)
• Add the BBMap folder to your PATH.
• Test by running bbduk.sh from another folder.

2. Install the latest version of fastq-tools.

• Clone the project into your local workspace (link above).
• Run ./autogen.sh from inside the fastq-tools directory to generate the the makefile.
• Run ./configure.sh && sudo make install to configure, build and install the tools.
• Note: if you don't have PCRE installed this will fail. It seems like re-installing the developer tools is the easiest solution to this problem.

If you follow the above steps, you have enough installed to run the insertion site identification script analyze_insertions.py. If this is all you want, then you are done. If you also want to use the DESeq analysis script calculate_enrichment.py then you also need to install the R runtime, the BioConductor and DESeq. You can follow instructions for installing R on their website (http://cran.r-project.org/bin/macosx/). You can install DESeq through BioConductor. BioConductor is available here: http://www.bioconductor.org/install/.

Running tests

• Install the nose test runner.
• sudo pip install nose
• Run all tests
• nosetests ./