Metadata-Version: 1.1
Name: starseqr
Version: 0.6.5
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| |Conda|
        
        =========
        STAR-SEQR
        =========
        RNA Fusion Detection and Quantification using STAR.
        
        Post-alignment run times are typically <20 minutes using 4 threads.  Development is still ongoing and several features are currently in the works. DNA breakpoint detection is still experimental.
        
        
        Installation
        ------------
        
        This package is tested under Linux using Python 2.7, 3.4, 3.5, and 3.6.
        
        You can install from Pypi. Please use a recent version of pip and cython:
        ::
        
            pip install -U pip
            pip install -U cython
            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:
        ::
        
            conda install starseqr
        
        
        **Additional Requirements**
         - biobambam2(https://github.com/gt1/biobambam2) or conda install biobambam
         - STAR(https://github.com/alexdobin/STAR). Must use >2.5.3a. conda install star
         - Velvet(https://github.com/dzerbino/velvet) or conda install velvet
         - samtools(https://github.com/samtools/samtools) or conda install samtools
         - Salmon(https://combine-lab.github.io/salmon/) or conda install salmon
         - UCSC utils(http://hgdownload.soe.ucsc.edu/admin/exe/) or conda install ucsc-gtftogenepred
         - gffread(http://ccb.jhu.edu/software/stringtie/dl/gffread-0.9.8c.tar.gz) or conda install gffread
        
        
        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
        
        
        Run STAR-SEQR
        --------------
        
        STAR-SEQR can perform alignment or utilize existing outputs from STAR. Note- STAR-SEQR alignment parameters have been tuned for fusion calling.
        
        
        **Python on OS**
        ::
        
             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
        
        **CWL**
        
        Note that `--name_prefix` must be a string basename in this case.
        ::
             cwltool ~/path/STAR-SEQR/devtools/cwl/starseqr_v0.6.5.cwl --fq1 /path/UHRR_1_2_5m_L4_1.clipped.fastq.gz --fq2 /path/UHRR_1_2_5m_L4_2.clipped.fastq.gz --star_index_dir /path/gencodev25lift37/STAR_INDEX --name_prefix test_cwl --transcript_gtf /path/gencodev25/gencode.v25lift37.annotation.gtf --genome_fasta /path/gencodev25/GRCh37.primary_assembly.genome.fa --mode 1 --worker_threads 8
        
        **DOCKER**
        
        Note that `-p` must be a fully qualified path in this case.
        ::
             docker run -it -v /mounts:/mounts eagenomics/starseqr:0.6.5 starseqr.py -1 /mounts/path/UHRR_1_2_5m_L4_1.clipped.fastq.gz -2 /mounts/path/UHRR_1_2_5m_L4_2.clipped.fastq.gz -p /mounts/path/test_docker  -i /mounts/path/gencodev25lift37/STAR_INDEX -g /mounts/path/gencodev25/gencode.v25lift37.annotation.gtf  -r /mounts/path/gencodev25/GRCh37.primary_assembly.genome.fa -m 1 -vv
        
        
        Outputs
        -------
        A BEDPE file is produced and is compatible with SMC-RNA Dream Challenge.
        
        Breakpoints.txt and Candidates.txt have the following columns:
        
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | **Values**          | **Description**                                                                                                                                                        |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | NAME                | Gene Symbols for left and right fusion partners                                                                                                                        |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | NREAD_SPANS         | The number of paired reads that are discordant spanning and suppor the fusion                                                                                          |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | NREAD_JXNLEFT       | The number of paired reads that are anchored on the left side of the gene fusion                                                                                       |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | NREAD_JXNRIGHT      | The number of paired reads that are anchored on the right side of the gene fusion                                                                                      |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | FUSION_CLASS        | Classification of fusion based on chromosomal location, distance and strand. [GENE_INTERNAL, TRANSLOCATION, READ_THROUGH, INTERCHROM_INVERTED, INTERCHROM_INTERSTRAND] |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | SPLICE_TYPE         | Classification of the fusion breakpoint. If on the exon boundary is CANONICAL, else NON-CANONICAL                                                                      |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | BRKPT_LEFT          | The 0-based genomic position of the fusion breakpoint for the left gene partner                                                                                        |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | BRKPT_RIGHT         | The 0-based genomic position of the fusion breakpoint for the right gene partner                                                                                       |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | LEFT_SYMBOL         | The left gene symbol                                                                                                                                                   |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | RIGHT_SYMBOL        | The right gene symbol                                                                                                                                                  |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | ANNOT_FORMAT        | The description of keys that are used in the ANNOT column. Similar to VCF FORMAT notation.                                                                             |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | LEFT_ANNOT          | The values described in the ANNOT_FORMAT column for the left gene breakpoint                                                                                           |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | RIGHT_ANNOT         | The values described in the ANNOT_FORMAT column for the right gene breakpoint                                                                                          |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | DISTANCE            | The genomic distance between breakpoints. Empty if a translocation.                                                                                                    |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | ASSEMBLED_CONTIGS   | The velvet assembly of the supporting chimeric reads                                                                                                                   |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | ASSEMBLY_CROSS_JXN  | A boolean value indicating if the assembly crosses the putative breakpoint                                                                                             |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | PRIMERS             | Primers left, right designed against the highest expressing predicted fusion transcript                                                                                |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | ID                  | Internal notation of STAR-SEQR breakpoints.                                                                                                                            |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | SPAN_CROSSHOM_SCORE | Homology score with range of [0-1] to indicate the probability of spanning chimeric reads mapping to both gene partners                                                |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | JXN_CROSSHOM_SCORE  | Homology score with range of [0-1] to indicate the probability of junction chimeric reads mapping to both gene partners                                                |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | OVERHANG_DIVERSITY  | The number of unique fragments that fall from left anchored split-reads onto the right gene and vice-versa.                                                            |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | MINFRAG20           | The number of overhang fragments that have at least 20 bases                                                                                                           |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | MINFRAG35           | The number of overhang fragments that have at least 35 bases                                                                                                           |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | TPM_FUSION          | Expression of the most abundant fusion transcript expressed in transcripts per million                                                                                 |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | TPM_LEFT            | Expression of the most abundant left transcript expressed in transcripts per million                                                                                   |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | TPM_RIGHT           | Expression of the most abundant right transcript expressed in transcripts per million                                                                                  |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | MAX_TRX_FUSION      | Highest expressing fusion transcript. Expression corresponds to TPM_FUSION                                                                                             |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        | DISPOSITION         | Values to indicate PASS or other specific reasons for failure                                                                                                          |
        +---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
        
        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/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
        
        .. |Conda| image:: https://anaconda.org/bioconda/starseqr/badges/installer/conda.svg
            :target: https://bioconda.github.io/recipes/starseqr/README.html
        
Keywords: rna,rna-seq,fusions,chimeric,star
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Environment :: Console
Classifier: License :: Other/Proprietary License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
