starseqr 0.3.0.4

RNA-Fusion Calling with STAR

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:

• https://github.com/pysam-developers/pysam

• https://github.com/hall-lab/svtools

• https://github.com/vishnubob/ssw

• https://github.com/libnano/primer3-py