conda tophat STAR

conda create -n tophat python = 2.7
conda install -c bioconda tophat
conda install bowtie2

http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#the-bowtie2-build-indexer

https://www.researchgate.net/post/How_do_I_get_TopHat_to_make_my_Bowtie2_index_files

Hi Benjamin,
As Terezinha Souza pointed out, you need to create the bowtie2 index for the genome first. You do not need to export $BOWTIE2_INDEXES. The transcriptome index you tried to create with the command, requires the genome bowtie2 index. Likewise for the alignment, you still need the genome bowtie2 index
First, start by removing the transcriptome data folder,
rm -rf transcriptome_data
Then:
bowtie2-build Tcas.fa Tcas
# this will create Tcas*bt2 in the current directory
# now create the transcriptome index
tophat2 -G Tcas.gff --transcriptome-index=transcriptome_data/Tcas Tcas
#now run tophat2 on reads test.fastq
tophat2 --transcriptome-index=transcriptome_data/Tcas Tcas test.fastq

yes library-type. Then you need to know the way the library was prepared. Currently the dUTP protocol is mostly used and for this you need to specify --library-type fr-firststrand. Default is fr-unstranded.
--library-type fr-firststrand