Hello, I have been running Tophat2 for a while and haven't had issues with it until now that my input is a paired-end, strand-specific data set. I run Tophat2 indicating strand specificity (--library-type=fr-firststrand), without the -G genes.gtf option and everything goes well. However, Tophat2 crashes when starting to map left reads if I include the -G option. Can somebody comment on whether this is a TopHat2 bug? Otherwise: are the --library-type and -G options mutually incompatible? Thanks, G
I think I had the same problem. If I am not wrong, it must have exited showing an error at -G, next error will be at --transcript-index. The solution is the order of the parameters you are giving.
Follow this order -
tophat -G path/gene.gff3 --transcriptome-index path/transcript-index-name path/genome-bowtie-index 1.fastq 2.fastq