I am going to run TopHat to map my rna-seq reads to human genome and I found that one of the option is to provide TopHat with the annotation GTF file " -G/--GTF <GTF/GFF3 file>" and I found the following note in tophat manual
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. You can get a list of the sequence names in a Bowtie index by typing:
bowtie-inspect --names your_index
So before using a known annotation file with this option please make sure that the 1st column in the annotation file uses the exact same chromosome/contig names (case sensitive) as shown by the bowtie-inspect command above.
So I checked the the first column in my GTF , but my question is how to use bowtie-inspect to check the index file (I mean which file should I use to check that)