Overview

HTTPS SSH

News

Please check out our new Google newsgroup for TAPIS: https://groups.google.com/forum/?hl=en#!forum/tapis

*July 13, 2016*

Version 1.2.1 released!

GMAP version of 2015-07-23 is not compatible with TAPIS as a bug in their software does not provide strand information for all alignments. We recommend using a more recent version. Thank you to Lianfeng Gu from Haixia Institute of Science and Technology (HIST) for bringing this to our attention!

Summay

TAPIS (Transriptome Analysis Pipeline from Isoform Sequencing) is a program for correcting and aligning long reads with/without second generation reads, transcript clustering, novel and full-length splice isoform detection, and identification and analysis of polyadenylation (poly(A)) and alternative poly(A) (APA).

Install

python setup.py build

python setup.py install

Note:

To install to a local set of python libraries use --home=/PATH/TO/LOCAL/LIBRARY

Required Packages

  • SpliceGrapher
  • bx-python
  • pysam
  • matplotlib
  • NumPy

Running

Align reads to reference genome using alignPacBio.py

Run analysis on aligned reads using run_tapis.py