Question: How to build Hisat2 index for human genome (GRCh37 )?
0
gravatar for Vasu
3.5 years ago by
Vasu490
Vasu490 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 • 6.9k views
ADD COMMENTlink modified 3.5 years ago by h.mon31k • written 3.5 years ago by Vasu490
3
gravatar for h.mon
3.5 years ago by
h.mon31k
Brazil
h.mon31k 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 3.5 years ago by h.mon31k

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

ADD REPLYlink written 3.5 years ago by Vasu490
2
gravatar for genomax
3.5 years ago by
genomax91k
United States
genomax91k wrote:

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

ADD COMMENTlink written 3.5 years ago by genomax91k

Thank you very much !!

ADD REPLYlink written 3.5 years ago by Vasu490
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