How to have reference sequence names of Rat(mRatBN7.2) indexes as chromosome names just like aws-indexes for Rat(Rnor6.0)

[Kauthar-Omar]

Hello!

I have built a bowtie index for Rat(mRatBN7.2) using reference sequence available on NCBI. I have the reference sequence names for the indexes as the sequence ids (checked with bowtie-inspect -n). I would like my reference sequence names for the indexes to be the chromosome names as in Rat(Rnor6.0) aws-indexes. It is important to have them as chromosome names for my down-stream analyses.

How do I have reference sequence names of the Rat(mRatBN7.2) indexes I build as chromosome names just like aws-indexes for Rat(Rnor6.0)?

Thank you.