NCBI genome annotation compatible with HISAT

Question

[rob.costa1234]

I am using a genome from NCBI will the annotation will be directly compatible with HISAT alignment , Do i need to change coordinates +1 or add chr?

[Sparrow_kop]

You just want to align the reads to transcriptom, so you need not to change coordinates. Also, the chromosome name can be 'chr1' or '1', you can just simple use the genome fasta to get the index file by hisat. Then hisat do everything for you.