Skip to content
Paired-end RNA-Seq splice site detection
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.gitattributes
.gitignore
README.md
passion-1.2.1.tar.gz

README.md

PASSion

PASSion uses the mapped read in a pair as anchor and then uses a high resolution algorithm, pattern growth, to remap the proximal and distal fragments of the unmapped read to a local region of the reference indicated by the mate. It is capable of identifying both known and novel canonical and non-canonical junctions with SNP or sequencing error tolerance. In addition, our package can discover differential and shared splicing patterns among multiple samples.

Installation

PASSION requires gcc >=4.3, SMALT, perl, and SAMtools to be pre-installed.

Go to PASSION directory to compile the component

cd  path_to_passion/PASSION
sh compile.sh

Go to SMALT directory, set the right binary version of smalt (according to your system) smalt-0.5.7

cp smalt_version smalt
(example:) cp smalt_x86_64 smalt

Install Samtools

Set SMALT, SAMtools and PASSION directory to PATH

Index the Reference

smalt index -k 13 -s 6 refindex reference.fa
samtools faidx reference.fa

Run PASSion

passion.pl -s insert_size -r read1.fq -f read2.fq -R reference.fa -I refindex   

Find differential splicing patterns in multiple samples

step1: edit a configure file. For example sample.txt

./s8_passion_output	s8
./s1_passion_output	s1
./s2_passion_output	s2

step2: run passion_diff.pl passion_diff.pl -f sample.txt

Example: discovery of junctions at chromosome 17 (sample.txt needs to be edited) cd path_to_testset/testset smalt index -k 13 -s 6 17 17.fa samtools faidx 17.fa passion.pl -s 200 -r read1.50.fq -f read2.50.fq -R 17.fa -I 17 -o s1_passion_output passion.pl -s 300 -r read1.75.fq -f read2.75.fq -R 17.fa -I 17 -o s2_passion_output passion.pl -s 500 -r read1.100.fq -f read2.100.fq -R 17.fa -I 17 -o s8_passion_output passion_diff.pl -f sample.txt Install

LINK

https://trac.nbic.nl/passion/
You can’t perform that action at this time.