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Old 06-22-2017, 10:41 PM   #1
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Location: Italy

Join Date: Oct 2012
Posts: 8
Default HISAT2: advantages of build index using annotated transcripts


after reading the paper, I am still not sure about what is the advantage of building an index for HISAT2 by calling hisat2-build with options —s and —exon instead of using the genome sequence only.

The online manual of HISAT2 tells that for the alignment phase it is possible to use the option --known-splicesite-infile and says: "Note that it is better to use indexes built using annotated transcripts (such as genome_tran or genome_snp_tran), which works better than using this option.”

But what 'better' means? Will be faster? Or will have more sensitivity? Or both?

In other words, if I do not build the index by giving annotated transcripts from a GTF file, and than I align by passing that GTF file, I loose only CPU time or I loose some alignments?

Thanks very much!

Last edited by dekontrol; 06-22-2017 at 10:46 PM.
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