Question: How to build Hisat2 index for human genome (GRCh37 )?
0
gravatar for Vasu
22 months ago by
Vasu320
Vasu320 wrote:

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

hisat2 rna-seq • 4.7k views
ADD COMMENTlink modified 22 months ago by h.mon24k • written 22 months ago by Vasu320
3
gravatar for h.mon
22 months ago by
h.mon24k
Brazil
h.mon24k wrote:

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.

ADD COMMENTlink written 22 months ago by h.mon24k

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

ADD REPLYlink written 22 months ago by Vasu320
2
gravatar for genomax
22 months ago by
genomax63k
United States
genomax63k wrote:

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

ADD COMMENTlink written 22 months ago by genomax63k

Thank you very much !!

ADD REPLYlink written 22 months ago by Vasu320
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