prapi 6.2.0

Transcriptome Analysis Pipeline for Isoform Sequencing

Prapi Summary

More Detail information is on http://www.bioinfor.org/tool/PRAPI/.

PRAPI is a one-stop solution for Iso-Seq analysis of analyze alternative transcription initiation (ATI), alternative splicing (AS), alternative cleavage and polyadenylation (APA), natural antisense transcripts (NAT), and circular RNAs (circRNAs) comprehensively.

Update

2019.9.6

Fix APA support number Bugs.

Installation

Basic prapi installation (python 2.7 support)

Before install,Please install these base.

$conda install -y -c bioconda bx-python

$conda install -y -c bioconda pycairo

$conda install -c bioconda pysam

$conda install -c bioconda gmap

$conda install -c biocodna samtools==0.1.19

$conda install -c bioconda gmap==2016.09.23

$conda install -c bioconda cufflinks==2.2.1

$conda install -c bioconda bioconductor-edger

$conda install -c bioconda bioconductor-degseq

$pip install scipy

$pip install fisher

$pip install CIRCexplorer

$wget http://www.bioinfor.org/tool/PRAPI/download/SpliceGrapher-0.2.5.tar.gz

$tar -xzvf SpliceGrapher-0.2.5.tar.gz

$cd SpliceGrapher-0.2.5

$python setup.py install

#After this,Please install prapi

$pip install prapi

####################################

#test file

wget http://www.bioinfor.org/tool/PRAPI/download/v2/test_v2.tar.gz

tar -xvzf test_v2.tar.gz

cd test_v2

sh run.sh

####################################

See more complete tutorials on the documentation page.

RNA

Further Documentation

Citation

Gao Y, Wang H, Zhang H, Wang Y, Chen J, Gu L, (2017), PRAPI: post-transcriptional regulation analysis pipeline for Iso-Seq.Bioinformatics,Bioinformatics, btx830,https://doi.org/10.1093/bioinformatics/btx830