Question: Advantage of making HISAT2 genome index with annotation file
gravatar for piyushjo
10 months ago by
piyushjo110 wrote:


I am trying to find a definitive answer to my problem: shall I use annotation file to make a genome index or not? In a bioinformatics workshop I attended the instructor said there is no fall out of not using the annotation file while making the index. I am aware that hisat2 website provides pre-built indices. However, I want to use gencode annotation files or lncipedia files which are not suitable for hisat2 provided indices.

I found a similar unanswered question on seqanswers

Any suggestion is highly appreciated!

ADD COMMENTlink modified 10 months ago by RamRS23k • written 10 months ago by piyushjo110
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