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Old 04-07-2016, 02:56 AM   #16
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Location: Paris

Join Date: Mar 2016
Posts: 2


Did you try to test an index like described :

--known-splicesite-infile <path>

With this mode, you can provide a list of known splice sites, which HISAT2 makes use of to align reads with small anchors.
You can create such a list using python genes.gtf > splicesites.txt, where is included in the HISAT2 package, genes.gtf is a gene annotation file, and splicesites.txt is a list of splice sites with which you provide HISAT2 in this mode. 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. It has no effect to provide splice sites that are already included in the indexes.
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