Question: HISAT2 build index
2
gravatar for saj98
3.2 years ago by
saj98110
saj98110 wrote:

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 error Error: could not open genome.2.ht2 and Error: Encountered internal HISAT2 exception (#1)

Kindly help

rna-seq assembly • 13k views
ADD COMMENTlink modified 3.2 years ago by h.mon31k • written 3.2 years ago by saj98110

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

ADD REPLYlink written 3.2 years ago by WouterDeCoster44k
12
gravatar for h.mon
3.2 years ago by
h.mon31k
Brazil
h.mon31k wrote:

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).

ADD COMMENTlink written 3.2 years ago by h.mon31k

Yes, I got it. Thank you so much

ADD REPLYlink written 3.2 years ago by saj98110

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

ADD REPLYlink written 3.2 years ago by WouterDeCoster44k
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