View Single Post
Old 04-07-2016, 02:56 AM   #16
nlapalu
Junior Member
 
Location: Paris

Join Date: Mar 2016
Posts: 2
Default

Hi,

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 hisat2_extract_splice_sites.py genes.gtf > splicesites.txt, where hisat2_extract_splice_sites.py 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.
nlapalu is offline   Reply With Quote