RNA-Fusion Calling with STAR
Project description
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:
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.