getting indexing files using hisat2-build
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.
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Ram
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Youngshil •
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Youngshil •
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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.