Metadata-Version: 1.0
Name: starseqr
Version: 0.3.0
Summary: RNA-Fusion Calling with STAR
Home-page: https://github.com/ExpressionAnalysis/STAR-SEQR
Author: Jeff Jasper
Author-email: jasper1918@gmail.com
License: Custom
Description: |Travis| |Pypi|
        
        =========
        STAR-SEQR
        =========
        RNA Fusion Detection using the STAR-Aligner. Post-alignment run times are typically <10 minutes using 4 threads. DNA breakpoint detection is also supported. Development is still ongoing and several features are currently in the works.
        
        
        Installation
        ------------
        
        This package is tested under Linux using Python 2.7, 3.4, and 3.5.
        
        You can install from Pypi:
        ::
        
            pip install starseqr
        
        Or build directly from Github by cloning the project, cd into the directory and run:
        ::
        
            python setup.py install
        
        Or from Docker:
        ::
        
            docker pull eagenomics/starseqr
        
        Or from Bioconda:
        ::
        
            **pending approval**
        
        
        **Additional Requirements**
         - biobambam2(https://github.com/gt1/biobambam2) or conda install biobambam
         - STAR(https://github.com/alexdobin/STAR) or conda install star
         - Velvet(https://github.com/dzerbino/velvet) or conda install velvet
         - samtools(https://github.com/samtools/samtools) or conda install samtools
         - UCSC utils(http://hgdownload.soe.ucsc.edu/admin/exe/) or conda install ucsc-gtftogenepred
        
        
        Build a STAR Index
        ------------------
        
        First make sure the dependencies are installed and generate a STAR index for your reference.
        
        **RNA Index**
        ::
        
             STAR --runMode genomeGenerate --genomeFastaFiles hg19.fa --genomeDir STAR_SEQR_hg19gencodeV24lift37_S1_RNA --sjdbGTFfile gencodeV24lift37.gtf --runThreadN 18 --sjdbOverhang 150 --genomeSAsparseD 1
        
        **DNA Index**
        ::
        
            STAR --runMode genomeGenerate --genomeFastaFiles hg19.fa --genomeDir ./ --runThreadN 18 --genomeSAsparseD 2
        
        
        Run STAR-SEQR
        ---------------
        
        STAR-SEQR can do the STAR alignments or utilize existing outputs.
        
        RNA-Fusions
        +++++++++++
        
        *Align and Call*
        ::
        
             starseqr.py -1 RNA_1.fastq.gz -2 RNA_2.fastq.gz -m 1 -p RNA_test -n RNA -t 12 -i path/STAR_INDEX -g gencode.gtf -r hg19.fa -vv
        
        *Call Only*::
        
             starseqr.py -ss RNA.Chimeric.out.sam -sj RNA.Chimeric.out.junction -p RNA_test -n RNA -t 12 -i path/STAR_INDEX -g gencode.gtf -r hg19.fa -vv
        
        DNA-Breakpoints
        +++++++++++++++
        
        *Align and Call*
        ::
        
            starseqr.py -1 DNA_1.fastq.gz -2 DNA_2.fastq.gz -m 0 -p DNA_test -n DNA -j 2 -s 1 -t 12 -i path/STAR_INDEX_DNA --ann_source gencode -vv
        
        *Call Only*
        ::
        
            starseqr.py DNA.Chimeric.out.sam -sj DNA.Chimeric.out.junction  -p DNA_test -n DNA -j 2 -s 1 -t 12 -i path/STAR_INDEX_DNA --ann_source gencode -vv
        
        Feedback
        --------
        
        Yes! Please give us your feedback, raise issues, and let us know how the tool is working for you. Pull requests are welcome.
        
        Contributions
        -------------
        
        This project builds of the groundwork of other public contributions. Namely:
        
        - https://github.com/pysam-developers/pysam
        - https://github.com/hall-lab/svtools
        - https://github.com/vishnubob/ssw
        - https://github.com/libnano/primer3-py
        
        
        
        .. |Travis| image:: https://travis-ci.org/ExpressionAnalysis/STAR-SEQR.svg?branch=master
            :target: https://travis-ci.org/ExpressionAnalysis/STAR-SEQR
        
        .. |Pypi| image:: https://badge.fury.io/py/starseqr.svg
            :target: https://badge.fury.io/py/starseqr
        
        
Keywords: rna,rna-seq,fusions,chimeric,star
Platform: UNKNOWN
