alignment-tools

From version 0.2.0, INTEGRATE is supporting more RNA-Seq reads alignment tools. For example, GSNAP and STAR.

example commands of running GSNAP:

gsnap -d hg19 -D hg19.gmap_index/ --format=sam --nthreads=12 -s hg19.splicesites.iit 1.fastq 2.fastq > gsnap.sam

samtools view -Sb -o gsnap.bam gsnap.sam

samtools sort gsnap.bam gsnap.sort

samtools index gsnap.sort.bam

example commands of running STAR:

STAR --runThreadN 12 --genomeDir hg19.star.index/ --readFilesIn 1.fastq 2.fastq --outFileNamePrefix star --chimSegmentMin 18

samtools sort star.chimeric.mapped.bam star.chimeric.mapped.sort

samtools index star.chimeric.mapped.sort.bam

example command of running INTEGRATE using BAMs from GSNAP:

Integrate fusion hg19.fa ensembl.txt bwts/ gsnap.sort.bam gsnap.sort.bam wgs.tumor.bam wgs.normal.bam

example command of running INTEGRATE using BAMs from STAR:

Integrate fusion hg19.fa ensembl.txt bwts/ star.chimeric.mapped.sort.bam star.chimeric.mapped.sort.bam wgs.tumor.bam wgs.normal.bam

Note

for a command such as:
Integrate fusion hg19.fa ensembl.txt bwts/ 1.mapped.bam 2.not-mapped.bam
INTEGRATE 0.2.0 takes mapped encompassing reads, soft-clipped and/or hard-clipped spanning reads, and reads serve as anchor (i.e mate not mapped) from 1.mapped.bam. INTEGRATE 0.2.0 takes the not mapped mates from 2.not-mapped.bam.

We have tested running INTEGRATE 0.2.0 with BAMs from TopHat2, GSNAP, and STAR.