Hi all,

I am trying to index my bacterial genome using Hisat2 following the RNA-SEQ analysis workflow

I wonder which genome file format I should use for indexing.

I tried indexing both files;

1. cds_from_genomic.fna (named genome1)
2. _genomic.fna (named genome2)

Using the command line ; hisat2-build genom1.fna indexed-genome

as expected it generated 8 (indexed-genome.fna.ht2) files

indexed-genome.fna.1.ht2
indexed-genome.fna.2.ht2
indexed-genome.fna.3.ht2
indexed-genome.fna.4.ht2
indexed-genome.fna.5.ht2
indexed-genome.fna.6.ht2
indexed-genome.fna.7.ht2
indexed-genome.fna.8.ht2

Using the command line;

hisat2 -x indexed-genome -1 TF_paired.fq.gz -2 TR_paired.fq.gz -S T1-1_hits.sam

I got T1-1_hits.sam file, with size 0, along with this error ;

Could not locate a HISAT2 index corresponding to basename "indexed-genome"
Error: Encountered internal HISAT2 exception (#1)

So, did I choose the wrong genome-file.

Or I should use an alternative pipeline like using bowtie over Hisat2 for bacterial RNA-SEQ analysis?

Thank you in advance,