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Old 04-30-2012, 01:32 AM   #1
Location: Germany

Join Date: Sep 2009
Posts: 21
Default tophat2 fusions.out empty

Dear Tophat user,

I'm trying to run tophat2 on my RNA seq data using command line

/programs/tophat-2.0.0.Linux_x86_64/tophat2 --bowtie1 -g 2 -r 26 -a 8 -m 0 --no-novel-juncs -j /annotation/EXONS.juncs --fusion-search --fusion-min-dist 100000 --fusion-anchor-length 10 --fusion-read-mismatches 0 -o P100 /annotation/hg19 /data/s_118_5.read1.fastq /data/s_118_5.read2.fastq

I got no errors but fusions.out file is empty. Do you have any idea what could be wrong?

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