RNA-Fusion Calling with STAR
Project description
STAR-SEQR
RNA Fusion Detection using the STAR-Aligner
Installation
- Required
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
Install:
python setup.py install
Usage
Generate a STAR index as follows:
- 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 as follows:
- RNA
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
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
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