Differences in HISAT2 indexes for download
Hi all, hope you guys are doing fine in the pandemic.
So I have just recently beginning to move into computational biology stuff (and found it amazing) and one of the first things Im trying to do is to map fastq files against the reference human genome. For that I’m using HISAT2 (because I’m running it on my own PC :/). I have done and ok mapping using the index “genome_tran” available in hisat2 own repository (daehwankimlab.github.io/hisat2/download/). But then after discussing a little bit I got really confused regarding the other indexes availabe (“genome” and “genome_snp” for example) and I could not understand the difference between them in the table at the end of the page. Can someone give a light on this? They all map against the genome?
genome: HISAT2 index for reference;
genome_snp: HISAT2 Graph index for reference plus SNPs;
genome_tran: HISAT2 Graph index for reference plus transcripts;
genome_snp_tran: HISAT2 Graph index for reference plus SNPs and transcripts;
For example, if I’m mapping against genome_snp, will I not get the transcripts levels bc they are only available in “genome_tran”?
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