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

Question

[Vasu]

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

Answer 1

[h.mon]

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.

[Vasu]

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

Answer 2

[GenoMax]

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

[Vasu]

Thank you very much !!