Install Seq2Fun

Seq2Fun was written in C/C++11 and can be installed on Linux or Mac OS X (with Xcode and Xcode Command Line Tools installed). We have tested Seq2Fun on Ubuntu (16.04 LTS and above) and macOS Catalina.

  1. Download & compile

    Click here to check and download all Seq2Fun stable releases (including version 1). The latest development version is hosted on GitHub. After download, from within the folder containing the downloaded package, issue the following commands:

    >tar -xvzf seq2fun_v*.tar.gz
    >cd Seq2fun/src/
    >make clean
    >make

    or the latest version (you need to follow instruction in https://github.com/xia-lab/Seq2Fun)
    >git clone https://github.com/xia-lab/Seq2Fun.git
    >cd Seq2Fun/src/
    >make clean
    >make

  2. Run a small test

    There are four sub folders under seq2fun - src, bin, database and testdata. The bin folder contains the binary code we just complied. The testdata contains a small test data from the Case Study. From within the testdata folder, issue the following commands:

    >../bin/seq2fun --sampletable sample.txt --tfmi example.fmi --genemap example_annotation.txt -w 8 --profiling -V --outputMappedCleanReads --outputReadsAnnoMap

    The progress will be displayed on the terminal. The screenshot below (from Ubuntu 20.04.3 LTS) shows the last few lines:

    You will see many files generated in the current folder:

  3. Submit gene abundance table to our website-based tool NetworkAnalyst (optional) for comprehensive data analysis and visual exploration.

    Seq2Fun generates several main files of s2f gene abundance table
    All_sample_s2fid_abundance_table.txt, All_sample_s2fid_abundance_table_submit_2_networkanalyst.txt, All_sample_annotation_submit_2_networkanalyst.txt, the last two can be used to submit to NetworkAnalyst.

    Note: please do not submit the tables generated by the testdata to NetworkAnalyst for the downstream analysis. This abundance table will not generate any biologically meaningful results because it is a just subset sample of the original data.
    Please go to NetworkAnalyst and select the example data DC cormorant toxicity for testing.