Alignment to ref genome

Question

[amy16]

I have generated the genome index using default options in HISAT2. now for the alignment purpose which if the output index files should i specify ?

[amy16]

What does the option wrapper means in hisat2?

Answer 1

[biplab]

You just need to specify the basename (part of the filename common to all of your index files) of index files. For example using genome.fa file as input in hisat2-buil we get these files as output(genome.1.ht2 genome.2.ht2 genome.3.ht2 genome.4.ht2 genome.5.ht2 genome.6.ht2 genome.7.ht2 genome.8.ht2). You just need to specify path to the index directory and basename(genome).

[amy16]

Thank you for the reply. Will try it now

[WouterDeCoster]

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