Please note: TopHat has a number of parameters and options, and their default values are tuned for processing mammalian RNA-Seq reads. If you would like to use TopHat for another class of organism, we recommend setting some of the parameters with more strict, conservative values than their defaults. The default is 70. -I/—max-intron-length
Please note that the values in the first column of the provided GTF/GFF file (column which indicates the chromosome or contig on which the feature is located), must match the name of the reference sequence in the Bowtie index you are using with TopHat. Analyze the daily evolution of requirement test coverage for a release. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction.