hello i indexed genome by bowtie2 and then use them to tophat2 but still give error .....
tophat2 -p 4 -r 200 --mate-std-dev 50 -G '/media/mra/4A3B44B64CA65A93/propooooooosssssssssal SNP/DATA/Genom/hashie nevisi/Apis_mellifera.GCA_000002195.1.32.gtf' -o '/media/mra/4A3B44B64CA65A93/propooooooosssssssssal SNP/DATA/drone larvae/SRR1571716/Tophat/tophat_out_SRR1571716' ref '/media/mra/4A3B44B64CA65A93/propooooooosssssssssal SNP/DATA/Genom/refrense genome/Bowtie2/indexed-refrence-genome.fa' '/media/mra/4A3B44B64CA65A93/propooooooosssssssssal SNP/DATA/drone larvae/SRR1571716/Trimmomatic/80/SRR1571716-1.trimmed.fastq.gz' '/media/mra/4A3B44B64CA65A93/propooooooosssssssssal SNP/DATA/drone larvae/SRR1571716/Trimmomatic/80/SRR1571716-2.trimmed.fastq.gz'
[2016-10-31 02:16:16] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2016-10-31 02:16:16] Checking for Bowtie
Bowtie version: 2.1.0.0
[2016-10-31 02:16:16] Checking for Samtools
Samtools version: 0.1.19.0
[2016-10-31 02:16:16] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (ref.*.bt2)
Please don't use spaces in file/directory names. That can only lead to trouble with TopHat. I suggest that you replace them with "_" so you can remove the single quotes you have had to use everywhere.
You are also using a 2+ year old version of TopHat which you should try and upgrade to the latest.