I am trying to use tophat-fusion for gene fusion detection.
my data (fastq files) are paired-end, and I have fastq files from multiple lanes, and they are compressed. (fastq.gz).
I am wondering (1) if tophat can take fastq files from multiple lanes in one command line as STAR can; (2) can tophat take fastq.gz files?
Because of the size of the data, it's difficult for me to unzip the fastq files, and merge the ones from multiple lanes into one, it will be not efficient.
Thanks for your help!