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What is the difference between HISAT2 index "genome.tran" and "genome"

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

hisat2 rna-seq index
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updated by vermack • vermack • written by Chevy Xu • Chevy Xu

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。

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written by li.anlin666 • li.anlin666

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

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written by GenoMax GenoMax

Google Translate says
google translate

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written by Ram Ram

1 answer

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
• 0 views • link
written by WouterDeCoster WouterDeCoster

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?

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written by lakhujanivijay lakhujanivijay

You will likely need the genome_tran.

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written by vermack • vermack

Does genome not contain any info on snp/transcripts?

• 1 views • link
written by Arindam Ghosh Arindam Ghosh

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