getting indexing files using hisat2-build
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4 months ago
Youngshil • 0

I used the following code to make index:

/media/share/tools/hisat2/hisat2-build -p 8 /media/share/refgenome/goldenHgenome/GCF_017639785.1_BCM_Maur_2.0_genomic.fa IndexGoldenHamster


same as:

hisat2-build -p 8 [reference genome] [Index name]


and as a result, I got: ﻿ Indexname.1.ht2

Indexname.2.ht2

Indexname.3.ht2

Indexname.4.ht2

﻿ But from my understanding, I am supposed to have 8 files of them.... Not really sure why I am only getting 4 index files..

hisat2 hisat2-build bioinformatics indexing • 365 views
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I think the number of the files generated depends on the genome size. But regarding the index name, make sure you did run the correct command (as above) because the command seems to be correct.