Entering edit mode
9.2 years ago
styrmll
•
0
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
Did you read the documentation here?