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RNA-Fusion Calling with STAR

Project description

|Travis| |Pypi| |Conda| |Last|

=========
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 -c bioconda starseqr


**Additional Requirements**
- biobambam2(https://github.com/gt1/biobambam2) or conda install -c bioconda biobambam
- STAR(https://github.com/alexdobin/STAR). Must use >2.5.3a. conda install -c bioconda star
- Velvet(https://github.com/dzerbino/velvet) or conda install -c bioconda velvet
- samtools(https://github.com/samtools/samtools) or conda install -c bioconda samtools
- Salmon(https://combine-lab.github.io/salmon/) or conda install -c bioconda salmon
- UCSC utils(http://hgdownload.soe.ucsc.edu/admin/exe/) or conda install -c bioconda ucsc-gtftogenepred
- gffread(http://ccb.jhu.edu/software/stringtie/dl/gffread-0.9.8c.tar.gz) or conda install -c bioconda 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 -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_v0.6.6.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

**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

.. |Last| image:: https://img.shields.io/github/last-commit/google/skia.svg
:target: https://github.com/ExpressionAnalysis/STAR-SEQR

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