HISAT2 build index

Question

[saj98]

Hello I am trying to build my index to HISAT2 using the following command

hisat2-build rn6_ercc/genome.1.ht2,genome.2.ht2,genome.3.ht2,genome.4.ht2,genome.5.ht2,genome.6.ht2,genome.7.ht2,genome.8.ht2 ht2_base

I got the following errors

Error: could not open genome.2.ht2

and

Error: Encountered internal HISAT2 exception (#1)

Kindly help

[WouterDeCoster]

Based on your command it looks like you already have the index files (.ht2)?

Answer 1

[h.mon]

You should build the index with something like:

hisat2-build genome.fa index_name

Where genome.fa is the fasta file of the genome you feed hisat2-build, and index_name will be the base name of the index files (*.ht2).

[saj98]

Yes, I got it. Thank you so much