Question: What is the difference between HISAT2 index "genome.tran" and "genome"
3
gravatar for Chevy Xu
21 months ago by
Chevy Xu30
Shanghai
Chevy Xu30 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 • 1.9k views
ADD COMMENTlink modified 16 months ago by li.anlin6660 • written 21 months ago by Chevy Xu30

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 16 months ago by li.anlin6660

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

ADD REPLYlink written 16 months ago by genomax71k

Google Translate says
google translate

ADD REPLYlink modified 16 months ago • written 16 months ago by RamRS24k
2
gravatar for WouterDeCoster
21 months ago by
Belgium
WouterDeCoster40k 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 21 months ago by WouterDeCoster40k
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 17 months ago by lakhujanivijay4.4k
1

Does genome not contain any info on snp/transcripts?

ADD REPLYlink modified 14 months ago • written 14 months ago by Arindam Ghosh170
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