RNA-Fusion Calling with STAR
Project 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. 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:
::
**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
=========
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. 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:
::
**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
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