Hi, I am new at using tophat2, in order to do that I am using a paper as a reference. In the paper they give the options they used [-r 25 --coverage-search -G --library-type fr-firststrand ], but I am getting an error. So this is the command line I use:
$ tophat -r 25 --coverage-search -G --library-type fr-firststrand /my_index directory/bowtie2/mm9 mysample.fastq &> tophat.log
In my log file it says:
Error: cannot find transcript file --library-type
I assume the error could be due to using -G but not providing an annotation, however in the paper they didn't provide anything other than they used mm9 genome for mapping. I have read tophat manual but couldn't figure out the reason of my error. Can anybody help me on this? Thanks!!