HISAT2 build index

Question

[saj98]

Hello everyone

I built rat genome index by using the command hisat2-build Rattus_norvegicus.Rnor_6.0.dna.chromosome.1.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.2.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.3.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.4.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.5.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.6.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.7.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.8.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.9.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.10.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.11.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.12.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.13.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.14.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.15.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.16.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.17.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.18.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.19.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.20.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.MT.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.X.fa,Rattus_norvegicus.Rnor_6.0.dna.chromosome.Y.fa,Rattus_norvegicus.Rnor_6.0.dna.nonchromosomal.fa ht2_base. However, I got the data with in Total time for call to driver() for forward index: 00:41:55. I wanna make sure I got right output. Could you please confirm for me?

Thanks for kind help

[GenoMax]

That does not tell us what you got in terms of files. Are there a total of 8 files that are non-empty that got generated?

[saj98]

Yes, I got 8 files that non of them empty, but the sizes are different. I typing what I got:

ht2_base.1.ht2, ht2_base.2.ht2, until file name is ht2_base.8.ht2.

Thanks

[GenoMax]

Try an alignment with the index then.

[saj98]

Yes it works. Thank you