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starseqr 0.6.3

RNA-Fusion Calling with STAR

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, 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:

conda install starseqr
Additional Requirements

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.

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

Outputs

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.

 
File Type Py Version Uploaded on Size
starseqr-0.6.3.tar.gz (md5) Source 2017-09-25 7MB