Error in Bowtie2

Question

[rasoulfarzaneh]

Hi The script I have is

tophat -p 4 --b2-very-sensitive -G '/home/rasoul/Desktop/Data/ngs/genome/annotation.gtf' /Home/rasoul/Desktop/Data/ngs/genome/genome '/Home/rasoul/Desktop/Data/ngs/SRR941816/keep16.gz' 



Error
[2020-04-05 18:15:48] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2020-04-05 18:15:48] Checking for Bowtie
          Bowtie version:    2.2.5.0
[2020-04-05 18:15:48] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files (/Home/rasoul/Desktop/Data/ngs/genome/genome.*.bt2l)

[GenoMax]

If you are trying to run a transcriptome only run with -G option then you are not supposed to provide reads for that run.

For example, in order to just prepare the transcriptome index files for a specific annotation, an initial, single TopHat run could be invoked like this:
tophat -G known_genes.gtf \
    --transcriptome-index=transcriptome_data/known \
    hg19

It also looks like you need to use /Home/rasoul/Desktop/Data/ngs/genome/ as the index base.

You should also consider switching to a newer aligner than TopHat.