bowtie2-inspect

[mdb@wistar]

I want to use tophat2 with reference gtf file from UCSC genome browser for which I am supposed to check that the values in the first column of the provided GTF must match the name of the reference sequence in the Bowtie index.
But to check this I tried the Bowtie2-inspect command:

bowtie2-inspect -s hg19index.fa as well as bowtie2-inspect -i hg19index.fa

I get this error:
"Could not locate a Bowtie index corresponding to basename "hg19index.fa""

But the index file worked fine with Bowtie2 as well as tophat2.

Am I making a mistake here, pl clarify,
thanks

[westerman]

Should work. Can you post an 'ls -l' of your directory please.

[mdb@wistar]

Thanks, i was able to solve the problem by renaming hg19.fa to hg19index.fa