Where:
Run hisat2 in the same folder as your RNA-seq reads. (Use File
--> OpenDir to open a new window in your RNA-seq reads folder.)
Input:
RNAseq reads: Before opening this menu, select RNA-seq
readfiles to be mapped to the genome. For paired-end reads, hisat2
words with pair of files. Files can be selected in pairs using
File --> guesspairs.py.
Choose any genome index file (eg. .ht2) - Choose any of
the .ht2 files created by hisat2-build. All .ht2 files that begin
with the same basename will be used for mapping your reads to the
genome.
Output:
The default "../bamfiles" means that output files will be written
to a folder in the parent folder (..) called bamfiles.
For every pair of read files in the input, there will be a single
bam file.