Question: What is the difference between HISAT2 index "genome.tran" and "genome"
4
gravatar for Chevy Xu
3.0 years ago by
Chevy Xu50
Shanghai
Chevy Xu50 wrote:

I try to use HISAT2 in order to map the reads to the genome, while HISAT2 pre-index the genome for users.

I saw that alternative sequences will affect the mapping results, does genome.tran index includes the alternative splicing and alternative sequences compare with genome index?

And what the difference between index genome and genome_tran?

which index file should I use in mapping process?

  1. genome

  2. genome_tran

  3. genome_snp_tran

Thanks for your answering

index rna-seq hisat2 • 3.1k views
ADD COMMENTlink modified 2.6 years ago by li.anlin6660 • written 3.0 years ago by Chevy Xu50

这要看你想要达到什么目的,要是单纯的比对,就用第一个 Genome的Indexes就好。

ADD REPLYlink written 2.6 years ago by li.anlin6660

Please post using English alphabet, otherwise this post may be deleted.

ADD REPLYlink written 2.6 years ago by GenoMax92k

Google Translate says
google translate

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by _r_am31k
2
gravatar for WouterDeCoster
3.0 years ago by
Belgium
WouterDeCoster44k wrote:

From https://ccb.jhu.edu/software/hisat2/index.shtml

  • genome: HFM index for reference
  • genome_snp: HGFM index for reference plus SNPs
  • genome_tran: HGFM index for reference plus transcripts
  • genome_snp_tran: HGFM index for reference plus SNPs and transcripts
ADD COMMENTlink written 3.0 years ago by WouterDeCoster44k
1

For a typical RNA-seq analysis, how do I decide which one to use? It surely depends on what I am looking for but I am not able to figure out. Can you please provide some hints?

ADD REPLYlink written 2.7 years ago by lakhujanivijay5.3k
1

Does genome not contain any info on snp/transcripts?

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Arindam Ghosh340
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