Dear All

I am very new to RNA seq analysis and stumbled over a question when going through tophat_fusion "Getting started" page. Does anyone know the benefit or disadvantage of including annotation option in the following command lines?

(with annotation option)

tophat \
  -o tophat_MCF7 \
  -G genes.gtf \
  -p 8 \
  --fusion-search \
  --keep-fasta-order \
  --bowtie1 \
  --no-coverage-search \
  -r 0 \
  --mate-std-dev 80 \
  --max-intron-length 100000 \
  --fusion-min-dist 100000 \
  --fusion-anchor-length 13 \
  --fusion-ignore-chromosomes chrM \
  /path/to/h_sapiens/bowtie_index \
  SRR064286_1.fastq SRR064286_2.fastq

(without annotation option)

tophat \
  -o tophat_MCF7 \
  -p 8 \
  --fusion-search \
  --keep-fasta-order \
  --bowtie1 \
  --no-coverage-search \
  -r 0 \
  --mate-std-dev 80 \
  --max-intron-length 100000 \
  --fusion-min-dist 100000 \
  --fusion-anchor-length 13 \
  --fusion-ignore-chromosomes chrM \
  /path/to/h_sapiens/bowtie_index \
  SRR064286_1.fastq SRR064286_2.fastq

Thank you very much for your help

Meng