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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?
Best
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?
Best