Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
cannot use "hisat2-build" command atonidas RNA Sequencing 2 05-23-2017 04:53 AM
How to generate VCF from HISAT2 pre-built SNP index? jol.espinoz Genomic Resequencing 0 04-30-2017 12:03 PM
To Build a New Index or Not To Build? arcolombo698 RNA Sequencing 0 11-30-2013 02:04 PM
Cufflinks Annotated Transcripts magarolo RNA Sequencing 1 12-08-2011 02:34 AM

Thread Tools
Old 06-22-2017, 11:41 PM   #1
Junior Member
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 11:46 PM.
dekontrol is offline   Reply With Quote

alignment, hisat, hisat2, indexing

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 12:51 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO