README.md

CAPTRE

This is the script repository for CAPTRE analysis (cap profiling for translational efficiency).

The repository includes scripts for the following tasks.

1. Identification of TSS-isoform pairs with significant divergent TE (bootstraping + FDR control)

2. Construction of 5p-UTRs isforms without alternative splicing

3. Sequence features responsible for TE regulation

Installation:

• CAPTRE requires

  • [Perl] (https://www.perl.org/) >=5.10 with
    • [Scalar-List-Utils] (http://search.cpan.org/~pevans/Scalar-List-Utils-1.45/) >=1.45
    • [Math-Random-OO] (http://search.cpan.org/~dagolden/Math-Random-OO-0.22/) >=0.22
  • [R] (https://www.r-project.org/) >=3.2 with
    • [Hmisc] (https://cran.r-project.org/web/packages/Hmisc/index.html)
  • [bedtools] (http://bedtools.readthedocs.io/en/latest/) >=2.17.0

• Download scripts

  git clone https://github.com/sunlightwang/CAPTRE.git

  then cd to each directory and refer to README.sh inside to run. Three folders for the three tasks are listed below:

  • altTSS_divTE
  • 3T3_5UTR_CS
  • Seq_feat

Contact:

Xi Wang (xi dot wang at mdc-berlin dot de)

Citation:

[1] Xi Wang*, Jingyi Hou*, Claudia Quedenau, Wei Chen (2016) [Pervasive isoform-specific translational regulation via alternative transcription start sites in mammals] (http://msb.embopress.org/content/12/7/875). Molecular Systems Biology, 12: 875.