#3 Integrate and GSNAP or START

[Sergey Mitrofanov]

Hi,
I couldn't start Integrate with mentiond RNA-Seq reads alignment tools: GSNAP and STAR (https://sourceforge.net/p/integrate-fusion/wiki/alignment-tools/). Help, please.

[Jin]

Hi, Please try this:

gsnap -d hg19 -D ./hg19.gmap_index/ --format=sam --nthreads=8 -s ./hg19.splicesites.iit 1.fq 2.fq > gsnap.sam
samtools view -Sb -o gsnap.bam gsnap.sam
samtools sort gsnap.bam gsnap.sort
samtools index gsnap.sort.bam
Integrate fusion hg19.fa annot.txt ./bwt gsnap.sort.bam gsnap.sort.bam

STAR --runThreadN 8 --genomeDir ./hg19.star --readFilesIn 1.fq 2.fq --outFileNamePrefix ./star --chimSegmentMin XX
samtools view -Sb -o starChimeric.bam starChimeric.out.sam
samtools sort starChimeric.bam starChimeric.sort
samtools index starChimeric.sort.bam
Integrate fusion hg19.fa annot.txt starChimeric.sort.bam starChimeric.sort.bam