{ "info": { "author": "Jeff Jasper", "author_email": "jasper1918@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: Console", "Intended Audience :: Science/Research", "License :: Other/Proprietary License", "Natural Language :: English", "Operating System :: OS Independent", "Programming Language :: Python", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: Implementation :: CPython", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "|Travis| |Pypi| |Conda| |Last|\n\n=========\nSTAR-SEQR\n=========\nRNA Fusion Detection and Quantification using STAR.\n\nPost-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.\n\n\nInstallation\n------------\n\nThis package is tested under Linux using Python 2.7, 3.4, 3.5, and 3.6.\n\nYou can install from Pypi. Please use a recent version of pip and cython:\n::\n\n pip install -U pip\n pip install -U cython\n pip install starseqr\n\nOr build directly from Github by cloning the project, cd into the directory and run:\n::\n\n python setup.py install\n\nOr from Docker:\n::\n\n docker pull eagenomics/starseqr\n\nOr from Bioconda:\n::\n\n conda install -c bioconda starseqr\n\n\n**Additional Requirements**\n - biobambam2(https://github.com/gt1/biobambam2) or conda install -c bioconda biobambam\n - STAR(https://github.com/alexdobin/STAR). Must use >2.5.3a. conda install -c bioconda star\n - Velvet(https://github.com/dzerbino/velvet) or conda install -c bioconda velvet\n - samtools(https://github.com/samtools/samtools) or conda install -c bioconda samtools\n - Salmon(https://combine-lab.github.io/salmon/) or conda install -c bioconda salmon\n - UCSC utils(http://hgdownload.soe.ucsc.edu/admin/exe/) or conda install -c bioconda ucsc-gtftogenepred\n - gffread(http://ccb.jhu.edu/software/stringtie/dl/gffread-0.9.8c.tar.gz) or conda install -c bioconda gffread\n\n\nBuild a STAR Index\n------------------\n\nFirst make sure the dependencies are installed and generate a STAR index for your reference.\n\n**RNA Index**\n::\n\n STAR --runMode genomeGenerate --genomeFastaFiles hg19.fa --genomeDir STAR_SEQR_hg19gencodeV24lift37_S1_RNA --sjdbGTFfile gencodeV24lift37.gtf --runThreadN 18 --sjdbOverhang 150 --genomeSAsparseD 1\n\n\nRun STAR-SEQR\n--------------\n\nSTAR-SEQR can perform alignment or utilize existing outputs from STAR. Note- STAR-SEQR alignment parameters have been tuned for fusion calling.\n\n\n**Python on OS**\n::\n\n starseqr.py -1 RNA_1.fastq.gz -2 RNA_2.fastq.gz -m 1 -p RNA_test -t 12 -i path/STAR_INDEX -g gencode.gtf -r hg19.fa -vv\n\n**CWL**\n\nNote that `--name_prefix` must be a string basename in this case.\n::\n cwltool ~/path/STAR-SEQR/devtools/cwl/starseqr_v0.6.6.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\n\n**DOCKER**\n\nNote that `-p` must be a fully qualified path in this case.\n::\n 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\n\n\nOutputs\n-------\nA BEDPE file is produced and is compatible with SMC-RNA Dream Challenge.\n\nBreakpoints.txt and Candidates.txt have the following columns:\n\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| **Values** | **Description** |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| NAME | Gene Symbols for left and right fusion partners |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| NREAD_SPANS | The number of paired reads that are discordant spanning and suppor the fusion |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| NREAD_JXNLEFT | The number of paired reads that are anchored on the left side of the gene fusion |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| NREAD_JXNRIGHT | The number of paired reads that are anchored on the right side of the gene fusion |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| FUSION_CLASS | Classification of fusion based on chromosomal location, distance and strand. [GENE_INTERNAL, TRANSLOCATION, READ_THROUGH, INTERCHROM_INVERTED, INTERCHROM_INTERSTRAND] |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| SPLICE_TYPE | Classification of the fusion breakpoint. If on the exon boundary is CANONICAL, else NON-CANONICAL |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| BRKPT_LEFT | The 0-based genomic position of the fusion breakpoint for the left gene partner |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| BRKPT_RIGHT | The 0-based genomic position of the fusion breakpoint for the right gene partner |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| LEFT_SYMBOL | The left gene symbol |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| RIGHT_SYMBOL | The right gene symbol |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| ANNOT_FORMAT | The description of keys that are used in the ANNOT column. Similar to VCF FORMAT notation. |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| LEFT_ANNOT | The values described in the ANNOT_FORMAT column for the left gene breakpoint |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| RIGHT_ANNOT | The values described in the ANNOT_FORMAT column for the right gene breakpoint |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| DISTANCE | The genomic distance between breakpoints. Empty if a translocation. |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| ASSEMBLED_CONTIGS | The velvet assembly of the supporting chimeric reads |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| ASSEMBLY_CROSS_JXN | A boolean value indicating if the assembly crosses the putative breakpoint |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| PRIMERS | Primers left, right designed against the highest expressing predicted fusion transcript |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| ID | Internal notation of STAR-SEQR breakpoints. |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| SPAN_CROSSHOM_SCORE | Homology score with range of [0-1] to indicate the probability of spanning chimeric reads mapping to both gene partners |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| JXN_CROSSHOM_SCORE | Homology score with range of [0-1] to indicate the probability of junction chimeric reads mapping to both gene partners |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| OVERHANG_DIVERSITY | The number of unique fragments that fall from left anchored split-reads onto the right gene and vice-versa. |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| MINFRAG20 | The number of overhang fragments that have at least 20 bases |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| MINFRAG35 | The number of overhang fragments that have at least 35 bases |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| TPM_FUSION | Expression of the most abundant fusion transcript expressed in transcripts per million |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| TPM_LEFT | Expression of the most abundant left transcript expressed in transcripts per million |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| TPM_RIGHT | Expression of the most abundant right transcript expressed in transcripts per million |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| MAX_TRX_FUSION | Highest expressing fusion transcript. Expression corresponds to TPM_FUSION |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n| DISPOSITION | Values to indicate PASS or other specific reasons for failure |\n+---------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------+\n\nFeedback\n--------\n\nYes! Please give us your feedback, raise issues, and let us know how the tool is working for you. Pull requests are welcome.\n\nContributions\n-------------\n\nThis project builds of the groundwork of other public contributions. 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