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How to build Hisat2 index for human genome (GRCh37 )?

Hello Everyone,

This is my first time using HISAT2 for alignment. I would like to map against GRCh37. Can anyone tell me how to build an index file for HISAT2?

Thank you

rna-seq hisat2
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updated by h.mon h.mon • written by Vasu Vasu

2 answers

Why don't you download pre-built indexes? For example here for Ensembl GRCh37 - you may also download genome_snp, genome_tran and / or genome_snp_tran, see the ftp for all files.

To learn how to build the index, read HISAT2 manual.

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written by h.mon h.mon

oh sorry, Didn't see this. Thanks a lot !!

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written by Vasu Vasu

Take a look at the Nature Protocols paper to get a comprehensive overview. Building indexes is covered here.

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written by GenoMax GenoMax

Thank you very much !!

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written by Vasu Vasu

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